Methods of treating cancer

ABSTRACT

The present invention relates to methods of treating cancer by administering the EZH2 inhibitor compounds and pharmaceutical compositions to subjects in need thereof. The present invention also relates to the use of such compounds for research or other non-therapeutic purposes.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/979,916, filed May 15, 2018, which is a continuation application ofU.S. application Ser. No. 15/598,262, filed May 17, 2017, which is acontinuation application of U.S. application Ser. No. 14/054,646, filedOct. 15, 2013 (now U.S. Pat. No. 9,688,665), which claims priority to,and the benefit of U.S. Provisional Application Nos. 61/714,045, filedOct. 15, 2012, 61/758,972, filed Jan. 31, 2013, 61/714,140, filed Oct.15, 2012, 61/714,145, filed Oct. 15, 2012, 61/780,703, filed Mar. 13,2013, and 61/786,277, filed Mar. 14, 2013. The contents of each of theseprovisional applications are incorporated herein by reference in theirentireties.

INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING

The contents of the text file named “41478-513001US_ST25.txt”, which wascreated on Jan. 10, 2014 and is 141 KB in size, are hereby incorporatedby reference in their entireties.

FIELD OF INVENTION

The present invention relates generally to the field of cancertreatment, and in particular, the treatment of cancer associated withthe SWI/SNF complex (i.e., SWI/SNF mediated cancer). More particularly,the present invention provides methods and compositions which treat,alleviate, prevent, diminish or otherwise ameliorate the symptoms ofcancer associated with the SWI/SNF complex.

BACKGROUND OF THE INVENTION

Disease-associated chromatin-modifying enzymes (e.g., EZH2) play a rolein diseases such as proliferative disorders, metabolic disorders, andblood disorders. Thus, there is a need for the development of smallmolecules that are capable of modulating the activity of EZH2.

SUMMARY OF THE INVENTION

The present invention provides a method for treating or alleviating asymptom of a SWI/SNF-associated cancer in a subject by administering toa subject in need thereof a therapeutically effective amount of an EZH2inhibitor, where the subject has a cancer selected from the groupconsisting of brain and central nervous system cancer, head and neckcancer, kidney cancer, ovarian cancer, pancreatic cancer, leukemia, lungcancer, lymphoma, myeloma, sarcoma, breast cancer, and prostate cancer.For example, the SWI/SNF-associated cancer is characterized by reducedexpression and/or loss of function of the SWI/SNF complex or one or morecomponents of the SWI/SNF complex.

For example, the subject has a cancer selected from the group consistingof medulloblastoma, malignant rhabdoid tumor, and atypicalteratoid/rhabdoid tumor.

For example, the one or more components are selected from the groupconsisting of SNF5, ATRX, and ARID1A.

For example, the loss of function is caused by a loss of functionmutation resulting from a point mutation, a deletion, and/or aninsertion.

For example, the subject has a deletion of SNF5.

For example, the subject has a mutation of ATRX selected from the groupconsisting of a substitution of asparagine (N) for the wild type residuelysine (K) at amino acid position 688 of SEQ ID NO: 5 (K688N), and asubstitution of isoleucine (I) for the wild type residue methionine (M)at amino acid position 366 of SEQ ID NO: 5 (M366I).

For example, subject has a mutation of ARID1A selected from the groupconsisting of a nonsense mutation for the wild type residue cysteine (C)at amino acid position 884 of SEQ ID NO: 11 (C884*), a substitution oflysine (K) for the wild type residue glutamic acid (E) at amino acidposition 966 (E966K), a nonsense mutation for the wild type residueglutamine (Q) at amino acid position 1411 of SEQ ID NO: 11 (Q1411*), aframe shift mutation at the wild type residue phenylalanine (F) at aminoacid position 1720 of SEQ ID NO: 11 (F1720fs), a frame shift mutationafter the wild type residue glycine (G) at amino acid position 1847 ofSEQ ID NO: 11 (G1847fs), a frame shift mutation at the wild type residuecysteine (C) at amino acid position 1874 of SEQ ID NO: 11 (C1874fs), asubstitution of glutamic acid (E) for the wild type residue asparticacid (D) at amino acid position 1957 (D1957E), a nonsense mutation forthe wild type residue glutamine (Q) at amino acid position 1430 of SEQID NO: 11 (Q1430*), a frame shift mutation at the wild type residuearginine (R) at amino acid position 1721 of SEQ ID NO: 11 (R1721fs), asubstitution of glutamic acid (E) for the wild type residue glycine (G)at amino acid position 1255 (G1255E), a frame shift mutation at the wildtype residue glycine (G) at amino acid position 284 of SEQ ID NO: 11(G284fs), a nonsense mutation for the wild type residue arginine (R) atamino acid position 1722 of SEQ ID NO: 11 (R1722*), a frame shiftmutation at the wild type residue methionine (M) at amino acid position274 of SEQ ID NO: 11 (M274fs), a frame shift mutation at the wild typeresidue glycine (G) at amino acid position 1847 of SEQ ID NO: 11(G1847fs), a frame shift mutation at the wild type residue P at aminoacid position 559 of SEQ ID NO: 11 (P559fs), a nonsense mutation for thewild type residue arginine (R) at amino acid position 1276 of SEQ ID NO:11 (R1276*), a frame shift mutation at the wild type residue glutamine(Q) at amino acid position 2176 of SEQ ID NO: 11 (Q2176fs), a frameshift mutation at the wild type residue histidine (H) at amino acidposition 203 of SEQ ID NO: 11 (H203fs), a frame shift mutation at thewild type residue alanine (A) at amino acid position 591 of SEQ ID NO:11 (A591fs), a nonsense mutation for the wild type residue glutamine (Q)at amino acid position 1322 of SEQ ID NO: 11 (Q1322*), a nonsensemutation for the wild type residue serine (S) at amino acid position2264 of SEQ ID NO: 11 (S2264*), a nonsense mutation for the wild typeresidue glutamine (Q) at amino acid position 586 of SEQ ID NO: 11(Q586*), a frame shift mutation at the wild type residue glutamine (Q)at amino acid position 548 of SEQ ID NO: 11 (Q548fs), and a frame shiftmutation at the wild type residue asparagine (N) at amino acid position756 of SEQ ID NO: 11 (N756fs).

The present invention also provides a method of treating or alleviatinga symptom of a SWI/SNF-associated cancer in a subject in need thereof by(a) determining the expression level of at least one gene selected fromthe group consisting of neuronal differentiation genes, cell cycleinhibition genes and tumor suppressor genes in a sample obtained fromthe subject; (b) selecting the subject having a decreased expressionlevel of at least one gene in step a; and (c) administering to thesubject selected in step b an effective amount of an EZH2 inhibitor,thereby treating or alleviating a symptom of cancer in the subject.

The present invention further provides a method of treating oralleviating a symptom of a SWI/SNF-associated cancer in a subject inneed thereof by (a) determining the expression level of at least onegene selected from the group consisting of hedgehog pathway genes, mycpathway genes and histone methyltransferase genesin a sample obtainedfrom the subject; (b) selecting the subject having an increasedexpression level of at least one gene in step a; and (c) administeringto the subject selected in step b an effective amount of an EZH2inhibitor, thereby treating or alleviating a symptom of cancer in thesubject.

For example, the cancer can be medulloblastoma, malignant rhabdoid tumoror atypical teratoid rhabdoid tumor.

For example, the neuronal differentiation gene is CD133, DOCK4, orPTPRK.

For example, the cell cycle inhibition gene is CKDN1A or CDKN2A.

For example, the tumor suppressor gene is BIN1.

For example, the hedgehog pathway gene is GLI1 or PTCH1.

For example, the myc pathway gene is MYC.

For example, the histone methyltransferase gene is EZH2.

The present invention also provides a method of inducing neuronaldifferentiation, cell cycle inhibition or tumor suppression bycontacting a cell with an EZH2 inhibitor. The EZH2 inhibitor may be inan amount sufficient to increase expression of at least one geneselected from the group consisting of CD133, DOCK4, PTPRK, CKDN1A,CDKN2A and BIN1.

The present invention also provides a method of inhibiting hedgehogsignaling by contacting a cell with an EZH2 inhibitor. The EZH2inhibitor can be in an amount sufficient to reduce expression of GLI1and/or PTCH1.

The present invention also provides a method of inducing gene expressionby contacting a cell with an EZH2 inhibitor. The EZH2 inhibitor can bein an amount sufficient to induce neuronal differentiation, cell cycleinhibition and/or tumor suppression. For example, the gene can be CD133,DOCK4, PTPRK, CKDN1A, CKDN2A or BIN1.

The present invention also provides a method of inhibiting geneexpression by contacting a cell with an EZH2 inhibitor. The EZH2inhibitor is in an amount sufficient to inhibit hedgehog signaling. Forexample, the gene can be GLI1 or PTCH1.

For example, the cell may have loss of function of SNF5, ARID1A, ATRX,and/or a component of the SWI/SNF complex.

For example, the loss of function is caused by a deletion of SNF5.

For example, the cell is a cancer cell. The cancer can bemedulloblastoma, malignant rhabdoid tumor or atypical teratoid rhabdoidtumor.

For example, the EZH2 inhibitor is Compound A having the followingformula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvatesthereof.

For example, the EZH2 inhibitor is Compound B having the followingformula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvatesthereof.

For example, the EZH2 inhibitor is Compound C having the followingformula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvatesthereof.

For example, the EZH2 inhibitor is Compound D having the followingformula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvatesthereof.

For example, the EZH2 inhibitor is Compound E having the followingformula:

stereoisomers thereof, or pharmaceutically acceptable salts or solvatesthereof.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. In the specification, thesingular forms also include the plural unless the context clearlydictates otherwise. Although methods and materials similar or equivalentto those described herein can be used in the practice or testing of thepresent invention, suitable methods and materials are described below.All publications, patent applications, patents and other referencesmentioned herein are incorporated by reference. The references citedherein are not admitted to be prior art to the claimed invention. In thecase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods and examples areillustrative only and are not intended to be limiting.

Other features and advantages of the invention will be apparent from thefollowing detailed description and claims.

BRIEF DESCRIPTIONS OF FIGURES

FIGS. 1A and 1B are a series of Western blot analyses of cell lines withwild type (RD and SJCRH30) and mutant SNF5.

FIGS. 2A-2E are a series of graphs establishing that SNF5 mutant celllines A204 (FIG. 2C), G401 (FIG. 2D) and G402 (FIG. 2E) selectivelyrespond to EZH2 compound (Compound E) compared to wild type cell linesRD (FIG. 2A) and SJCRH30 (FIG. 2B).

FIGS. 3A-3D are a series of bar graphs showing that G401 SNF mutant cellline is responding to Compound E after 7 days in soft agar compared towild type cells RD. FIG. 3A shows cell line RD (5,000 cells/well). FIG.3B shows G401 cells (5,000 cells/well). FIG. 3C shows G401 cells in 2Dgrowth. FIG. 3D shows G401 cells (10,000 cells/well).

FIGS. 4A-4D are four graphs showing that G401 SNF5 mutant cell line issensitive to Compound A in vitro. Wild type cell lines SJCRH30 (FIG. 4A)and RD (FIG. 4C) and SNF5 mutant cell lines G401 (FIG. 4B) and A204(FIG. 4D) were pretreated for 7 days with indicated concentrations ofCompound A and replated on day 0. Cell viability was determined byCellTiter-Glo® Luminescent Cell Viability Assay.

FIGS. 5A-5E are a series of graphs showing durable regressions in G401xenografts (malignant rhabdoid tumor model) with Compound A treatment.FIG. 5A shows tumor regressions induced by Compound A at the indicateddoses. FIG. 5B shows tumor regressions induced by twice dailyadministration of Compound A at the indicated doses. Data represent themean values±SEM (n=8). Compound administration was stopped on day 28.FIG. 5C shows the EZH2 target inhibition in G401 xenograft tumor tissuecollected from a parallel cohort of mice on day 21. Each point shows theratio of H3K27Me3 to total H3. Horizontal lines represent group meanvalues. BLLQ=below lower limit of quantification. FIGS. 5D and 5E showimmunohistochemical staining of tumor histone methylation of tumorsamples from the vehicle treated (FIG. 5D) and Compound A treated (FIG.5E) (at 125 mg/kg) mice.

FIG. 6 is a graph showing the locations of ATRX mutations identified inSCLC cell lines.

FIG. 7A is a graph showing that LNCAP prostate cancer cells displaydose-dependent cell growth inhibition with Compound E treatment invitro.

FIG. 7B is a graph showing IC50 value of Compound E at day 11 and day 14for WSU-DLCL2 and LNCAP cells.

FIGS. 8A-8C are three graphs establishing that ATRX mutant SCLC linesNCI-H446 (FIG. 8A), SW1271 (FIG. 8B) and NCI-H841 (FIG. 8C) areresponding to Compound E.

FIGS. 9A-9C are three microscopy images showing that SCLC line NCI-H841changes morphology after treatment with vehicle (FIG. 9A) or Compound Eat concentration of 4.1E-02 uM (FIG. 9B) or 3.3 uM (FIG. 9C).

FIGS. 10A-10F are a series of graphs showing effects of Compound A oncellular global histone methylation and cell viability. FIG. 10A showsthe chemical structure of Compound A. FIG. 10B illustrates theconcentration-dependent inhibition of cellular H3K27Me3 levels in G401and RD cells. FIGS. 10C through 10F illustrate the selective inhibitionof proliferation of SMARCB1-deleted G401 cells by Compound A in vitro(measured by ATP content). G401 (FIGS. 10C and 10D) and RD cells (FIGS.10E and 10F) were re-plated at the original seeding densities on day 7.Each point represents the mean for each concentration (n=3).

FIGS. 11A and 11B are a series of graphs showing biochemical mechanismof action studies. The IC₅₀ value of Compound A increases withincreasing SAM concentration (FIG. 11A) and is minimally affected byincreasing oligonucleosome concentration (FIG. 11B), indicatingSAM-competitive and nucleosome-noncompetitive mechanism of action.

FIGS. 12A and 12B are a series of immunoblots demonstrating verificationof SMARCB1 and EZH2 expression in cell lines and specificity of CompoundA for inhibition of cellular histone methylation. FIG. 12A shows celllysates analyzed by immunoblot with antibodies specific to SMARCB1, EZH2and Actin (loading control). FIG. 12B illustrates selective inhibitionof cellular H3K27 methylation in G401 and RD cells. Cells were incubatedwith Compound A for 4 days, and acid-extracted histones were analyzed byimmunoblot.

FIGS. 13A and 13B are a series of bar graphs demonstrating that CompoundA induces G₁ arrest and apoptosis in SMARCB1-deleted MRT cells. Cellcycle analysis (by flow cytometry) and determination of apoptosis (byTUNEL assay) in RD (FIG. 13A) or G401 cells (FIG. 13B) during incubationwith either vehicle or 1 μM Compound A for up to 14 days. G₁ arrest wasobserved as of day 7 and apoptosis was induced as of day 11. Data arerepresented as mean values±SEM (n=2). The DMSO control values shown arethe average±SEM from each time point. Cells were split and re-plated ondays 4, 7 and 11 at the original seeding density.

FIGS. 14A-14L are a series of graphs showing that Compound A induceschanges in expression of SMARCB1 regulated genes and cell morphology.FIG. 14A shows the basal expression of SMARCB1 regulated genes in G401SMARCB1-deleted cells, relative to RD control cells (measured by qPCR,n=2). FIGS. 14B-14K show the expression of GLI1 (FIG. 14B), PTCh1 (FIG.14C), DOCK4 (FIG. 14D), CD133 (FIG. 14E), PTPRK (FIG. 14F), BIN1 (FIG.14G), CDKN1A (FIG. 14H), CDKN2A (FIG. 14I), EZH2 (FIG. 14J), and MYC(FIG. 14K) genes in G401 and RD cells. The cells were incubated witheither DMSO or 1 μM Compound A for 2, 4 and 7 days. Gene expression wasdetermined by qPCR (n=2) and is expressed relative to the DMSO controlof each time point. FIG. 14L illustrates the morphology of G402 cellsthat were incubated with either DMSO (left panel) or 1 μM Compound A(right panel) for 14 days. Cells were split and re-plated to theoriginal seeding density on day 7.

FIGS. 15A-15D are a series of graphs demonstrating body weights, tumorregressions and plasma levels in G401 xenograft bearing mice treatedwith Compound A. FIG. 15A shows body weights that were determined twicea week for animals treated with Compound A on a BID schedule for 28days. Data are presented as mean values±SEM (n=16 until day 21, n=8 fromday 22 to 60). FIG. 15B shows tumor regressions induced by twice daily(BID) administration of Compound A for 21 days at the indicated doses(mean values±SEM, n=16). *p<0.05, **p<0.01, repeated measures ANOVA,Dunnett's post-test vs. vehicle. FIG. 15C shows the tumor weights of 8mice euthanized on day 21. ****p<0.0001, Fisher's exact test. FIG. 15Dshows plasma levels of Compound A. Plasma was collected 5 min before and3 h after dosing of Compound A on day 21, and compound levels weremeasured by LC-MS/MS. Animals were euthanized, and tumors were collected3 h after dosing on day 21. Tumor homogenates were generated andsubjected to LC-MS/MS analysis to determine Compound A concentrations.Note that tumor compound levels could not be determined from all animalsespecially in the higher dose groups because the xenografts were toosmall on day 21. Dots represent values for the individual animals;horizontal lines represent group mean values.

FIGS. 16A-16F are a series of graphs showing that Compound A eradicatesSMARCB1-deleted MRT xenografts in SCID mice. FIG. 16A illustrates tumorregressions induced by twice daily (BID) administration of Compound Afor 28 days at the indicated doses. Compound administration was stoppedon day 28 and tumors were allowed to re-grow until they reached 2000 mm³(data shown as mean values±SEM, n=8). FIG. 16B shows the EZH2 targetinhibition in G401 xenograft tumor tissue collected from mice euthanizedon day 21. Each point shows the ratio of H3K27Me3 to total H3, measuredby ELISA. Horizontal lines represent group mean values; grey symbols arevalues outside of the ELISA standard curve. FIGS. 16C-16F summarize thechange in gene expression in G401 xenograft tumor tissue collected frommice treated with Compound A for 21 days. The graphs correspond to genesCD133 (FIG. 16C), PTPRK (FIG. 16D), DOCK4 (FIG. 16E), and GLI1 (FIG.16F), respectively. Data are presented as fold change compared tovehicle±SEM (n=6, n=4 for 500 mg/kg group). *p<0.05, **p<0.01,****p<0.0001, vs. vehicle, Fisher's exact test.

DETAILED DESCRIPTION OF THE INVENTION

The present invention is based in part upon the discovery that EZH2inhibitors can effectively treat SWI/SNF-associated cancers that arecharacterized by altered expressions and/or loss of function of certainbiomarkers or genes. Specifically, tumors or tumor cells having alteredexpressions and/or loss of function of selected biomarkers or genesaresensitive to the EZH2 inhibitors of the present invention. Accordingly,the present invention provides methods of treating or alleviating asymptom of cancers in a subject by administering a therapeuticallyeffective amount of an EZH2 inhibitor to the subject, particulartreating cancers associated with altered expression and/or loss offunction of certain biomarkers or genes. For example, the biomarker isone component of the SWI/SNF complex. For example, the gene is selectedfrom the group consisting of neuronal differentiation genes, cell cyclegene inhibition genes, tumor suppressor genes, hedgehog pathway genes,myc pathway genes and histone methyltransferase genes.

The SWI/SNF complex in human includes at least evolutionarily conservedcore subunits and variant subunits. Evolutionarily conserved coresubunits include SNF5 (also called SMARCB1, INI1 or BAF47), SMARCA4(also known as BRM/SWI2-related gene 1, BRG1), BAF155, and BAF170.Variant subunits include BAF53 (A or B), BAF60 (A, B or C), BAF 57,BAF45 (A, B, C, or D). Other subunits include ARIDI1A (also known asSMARCF1), ARID1B, SMARCA2 (also known as brahma homologue, BRM), ATRX,BAF200, BAF180 (also known as PBRM1), and bromodomain-containing 7(BRD7). The at least one component of the SWI/SNF complex can by anycomponent of the complex, for example, the component/subunit describedherein or known in the art.

In any methods presented herein, neuronal differentiation gene may be,but is not limited to, CD133 (also called PROM1), DOCK4, PTPRK, PROM2,LHX1, LHX6, LHX9, PAX6, PAX7, VEFGA, FZD3B, FYN, HIF1A, HTRA2, EVX1,CCDC64, or GFAP.

In any methods presented herein, cell cycle inhibition gene may be, butis not limited to, CKDN1A, CDKN2A, MEN1, CHEK1, IRF6, ALOX15B, CYP27B1,DBC1, NME6, GMNN, HEXIM1, LATS1, MYC, HRAS, TGFB1, IFNG, WNT1, TP53,THBS1, INHBA, IL8, IRF1, TPR, BMP2, BMP4, ETS1, HPGD, BMP7, GATA3,NR2F2, APC, PTPN3, CALR, IL12A, IL12B, PML, CDKN2B, CDKN2C, CDKN1B,SOX2, TAF6, DNA2, PLK1, TERF1, GAS1, CDKN2D, MLF1, PTEN, TGFB2, SMAD3,FOXO4, CDK6, TFAP4, MAP2K1, NOTCH2, FOXC1, DLG1, MAD2L1, ATM, NAE1,DGKZ, FHL1, SCRIB, BTG3, PTPRK, RPS6KA2, STK11, CDKN3, TBRG1, CDC73,THAP5, CRLF3, DCUN1D3, MYOCD, PAF1, LILRB1, UHMK1, PNPT1, USP47, HEXIM2,CDK5RAP1, NKX3-1, TIPIN, PCBP4, USP44, RBM38, CDT1, RGCC, RNF167, CLSPN,CHMP1A, WDR6, TCF7L2, LATS2, RASSF1, MLTK, MAD2L2, FBXO5, ING4, orTRIM35.

In any methods presented herein, tumor suppressor gene may be, but isnot limited to, BIN1. As used herein, the term “tumor suppressor gene”has its commonly understood meaning in the art, i.e. a gene whoseexpression and normal function act to suppress the neoplastic phenotypeor induce apoptosis, or both. In some embodiments, tumor suppressorgenes include cell cycle inhibition genes. Exemplary categories of tumorsuppressors based on their functions include, but not limited to:

(1) genes that inhibit cell cycles;(2) genes that are coupling the cell cycle to DNA damage. When there isdamaged DNA in the cell, the cell should not divide. If the damage canbe repaired, the cell cycle can continue. If the damage cannot berepaired, the cell should initiate apoptosis (programmed cell death);(3) genes that prevent tumor cells from dispersing, block loss ofcontact inhibition, and inhibit metastasis. These genes and theirencoded proteins are also known as metastasis suppressors; and(4) DNA repair proteins. Mutations in these genes increase the risk ofcancer.

In any methods presented herein, hedgehog signaling pathway gene may be,but is not limited to, GLI1, PTCH1, SUFU, KIF7, GLI2, BMP4, MAP3K10,SHH, TCTN3, DYRK2, PTCHD1, or SMO.

In any methods presented herein, myc pathway gene may be, but is notlimited to, MYC NMI, NFYC, NFYB, Cyclin T1, RuvB-like 1, GTF2I, BRCA1,T-cell lymphoma invasion and metastasis-inducing protein 1, ACTL6A,PCAF, MYCBP2, MAPK8, Bcl-2, Transcription initiation protein SPT3homolog, SAP130, DNMT3A, mothers against decapentaplegic homolog 3, MAX,mothers against decapentaplegic homolog 2, MYCBP, HTATIP, ZBTB17,Transformation/transcription domain-associated protein, TADA2L, PFDNS,MAPK1, TFAP2A, P73, TAF9, YY1, SMARCB1, SMARCA4, MLH1, EP400 or let-7.

In any methods presented herein, histone methyltransferase gene may be,but is not limited to, EZH2.

Compounds of the present invention inhibit the histone methyltransferaseactivity of EZH2 or a mutant thereof and, accordingly, in one aspect ofthe invention, compounds disclosed herein are candidates for treating orpreventing certain conditions and diseases. The present inventionprovides methods for treating, preventing or alleviating a symptom ofcancer or a precancerous condition. The method includes administering toa subject in need thereof, a therapeutically effective amount of acompound of the present invention, or a pharmaceutically acceptablesalt, polymorph, solvate, or stereoisomeror thereof. Exemplary cancersthat may be treated include medulloblastoma, oligodendroglioma, ovarianclear cell adenocarcinoma, ovarian endomethrioid adenocarcinoma, ovarianserous adenocarcinoma, pancreatic ductal adenocarcinoma, pancreaticendocrine tumor, malignant rhabdoid tumor, astrocytoma, atypicalteratoid rhabdoid tumor, choroid plexus carcinoma, choroid plexuspapilloma, ependymoma, glioblastoma, meningioma, neuroglial tumor,oligoastrocytoma, oligodendroglioma, pineoblastoma, carcinosarcoma,chordoma, extragonadal germ cell tumor, extrarenal rhabdoid tumor,schwannoma, skin squamous cell carcinoma, chondrosarcoma, clear cellsarcoma of soft tissue, ewing sarcoma, gastrointestinal stromal tumor,osteosarcoma, rhabdomyosarcoma, epithelioid sarcoma, renal medullocarcinoma, diffuse large B-cell lymphoma, follicular lymphoma and nototherwise specified (NOS) sarcoma. Alternatively, cancers to be treatedby the compounds of the present invention are non NHL cancers.

The present invention further provides the use of a compound of thepresent invention, or a pharmaceutically acceptable salt, polymorph orsolvate thereof in the treatment of cancer or precancer, or, for thepreparation of a medicament useful for the treatment of such cancer orpre-cancer. Exemplary cancers that may be treated includemedulloblastoma, oligodendroglioma, ovarian clear cell adenocarcinoma,ovarian endomethrioid adenocarcinoma, ovarian serous adenocarcinoma,pancreatic ductal adenocarcinoma, pancreatic endocrine tumor, malignantrhabdoid tumor, astrocytoma, atypical teratoid rhabdoid tumor, choroidplexus carcinoma, choroid plexus papilloma, ependymoma, glioblastoma,meningioma, neuroglial tumor, oligoastrocytoma, oligodendroglioma,pineoblastoma, carcinosarcoma, chordoma, extragonadal germ cell tumor,extrarenal rhabdoid tumor, schwannoma, skin squamous cell carcinoma,chondrosarcoma, clear cell sarcoma of soft tissue, ewing sarcoma,gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma,epithelioid sarcoma, renal medullo carcinoma, diffuse large B-celllymphoma, follicular lymphoma and not otherwise specified (NOS) sarcoma.Alternatively, the compound of the present invention can be used for thetreatment of non NHL cancers, or, for the preparation of a medicamentuseful for the treatment of non NHL cancers.

The compounds of this invention can be used to modulate protein (e.g.,histone) methylation, e.g., to modulate histone methyltransferase orhistone demethylase enzyme activity. The compounds of the invention canbe used in vivo or in vitro for modulating protein methylation. Basedupon the surprising discovery that methylation regulation by EZH2involves in tumor formation, particular tumors bearing alteredexpression and/or loss of function of selected biomarkers/genes, thecompounds described herein are suitable candidates for treating thesediseases, i.e., to decrease methylation or restore methylation toroughly its level in counterpart normal cells.

In some embodiments, compounds of the present invention can selectivelyinhibit proliferation of the SWI/SNF complex associated tumor or tumorcells (as shown in FIGS. 1-9). Accordingly, the present inventionprovides methods for treating, preventing or alleviating a symptom ofthe SWI/SNF complex associated cancer or a precancerous condition by acompound of the present invention, or a pharmaceutically acceptablesalt, polymorph or solvate thereof. The present invention furtherprovides the use of a compound of the present invention, or apharmaceutically acceptable salt, polymorph or solvate thereof in thetreatment of the SWI/SNF complex associated cancer or a precancercondition, or, for the preparation of a medicament useful for thetreatment of such cancer or pre-cancer.

Also provided in the present invention are methods for determiningresponsiveness of a subject having a cancer to an EZH2 inhibitor. Themethod includes the steps of obtaining a sample (a nucleic acid sampleor a protein sample) from the subject and detecting reduced expression,haploinsufficiency, and/or loss of function of at least one component ofthe SWI/SNF complex, detecting the expression and/or function of thiscomponent, and the presence of such reduced expression,haploinsufficiency, and/or loss of function indicates that the subjectis responsive to the EZH2 inhibitor. The term “sample” means anybiological sample derived from the subject, includes but is not limitedto, cells, tissues samples, body fluids (including, but not limited to,mucus, blood, plasma, serum, urine, saliva, and semen), tumor cells, andtumor tissues. Samples can be provided by the subject under treatment ortesting. Alternatively samples can be obtained by the physicianaccording to routine practice in the art.

The present invention also provides methods for determiningpredisposition of a subject to a cancer or a precancerous condition byobtaining a sample from the subject and detecting reduced expression,haploinsufficiency, and/or loss of function of at least one component ofthe SWI/SNF complex, and the presence of such reduced expression,haploinsufficiency, and/or loss of function indicates that the subjectis predisposed to (i.e., having higher risk of) developing the cancer orthe precancerous condition compared to a subject without such loss offunction of the at least one component of the SWI/SNF complex.

The term “predisposed” as used herein in relation to cancer or aprecancerous condition is to be understood to mean the increasedprobability (e.g., at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%,80%, 90%, 100%, 150%, 200%, or more increase in probability) that asubject with reduced expression, haploinsufficiency, and/or loss offunction of at least one component of the SWI/SNF complex, will suffercancer or a precancerous condition, as compared to the probability thatanother subject not having reduced expression, haploinsufficiency,and/or loss of function of at least one component of the SWI/SNFcomplex, will suffer cancer or a precancerous condition, undercircumstances where other risk factors (e.g., chemical/environment,food, and smoking history, etc.) for having cancer or a precancerouscondition between the subjects are the same.

“Risk” in the context of the present invention, relates to theprobability that an event will occur over a specific time period and canmean a subject's “absolute” risk or “relative” risk. Absolute risk canbe measured with reference to either actual observation post-measurementfor the relevant time cohort, or with reference to index valuesdeveloped from statistically valid historical cohorts that have beenfollowed for the relevant time period. Relative risk refers to the ratioof absolute risks of a subject compared either to the absolute risks oflow risk cohorts or an average population risk, which can vary by howclinical risk factors are assessed. Odds ratios, the proportion ofpositive events to negative events for a given test result, are alsocommonly used (odds are according to the formula p/(1-p) where p is theprobability of event and (1-p) is the probability of no event) tono-conversion.

Accordingly, the present invention provides personalized medicine,treatment and/or cancer management for a subject by genetic screening ofreduced expression, haploinsufficiency, and/or loss of function of atleast one component of the SWI/SNF complex in the subject. For example,the present invention provides methods for treating, preventing oralleviating a symptom of cancer or a precancerous condition bydetermining responsiveness of the subject to an EZH2 inhibitor and whenthe subject is responsive to the EZH2 inhibitor, administering to thesubject a therapeutically effective amount of the EZH2 inhibitor, or apharmaceutically acceptable salt, solvate, or stereoisomeror thereof.The responsiveness is determined by obtaining a sample from the subjectand detecting reduced expression, haploinsufficiency, and/or loss offunction of at least one component of the SWI/SNF complex (such as SNF5,ARID1A or ATRX), and the presence of such loss of function indicatesthat the subject is responsive to the EZH2 inhibitor.

In other example, the present invention provides methods of cancermanagement in a subject by determining predisposition of the subject toa cancer or a precancerous condition periodically. The methods includesteps of obtaining a sample from the subject and detecting reducedexpression, haploinsufficiency, and/or loss of function of at least onecomponent of the SWI/SNF complex, and the presence of such reducedexpression, haploinsufficiency, and/or loss of function indicates thatthe subject is predisposed to developing the cancer or the precancerouscondition compared to a subject without such reduced expression,haploinsufficiency, and/or loss of function of the at least onecomponent of the SWI/SNF complex.

In merely illustrative embodiments, the methods of treatment presentedherein include steps of (a) collecting a nucleic acid sample or aprotein sample from a biological sample obtained from a subject, (b)measuring the expression level or function level of a component of theSWI/SNF complex in the sample, (c) measuring the expression level orfunction level of the component of the SWI/SNF in a control sample; (d)comparing the expression level or the function level of the componentmeasured in step (b) in the tested sample to the expression level or thefunction level of the component measured in step (c) in the controlsample (or a reference value); (e) identifying the subject as acandidate for treatment when the expression level or the function levelof the component measured in step (b) is reduced or lost (e.g.,haploinsufficiency or loss of function) compared to the expression levelor the function level of the component measured in step (c); and (f)administering a therapeutically effective amount of an EZH2 inhibitor tothe subject identified in step (e) or selecting a treatment regimen forthe subject identified in step (e). The expression level or the functionlevel of component in the subject sample is reduced, for example, 10%,25%, 50% or 1-, 2-, 5- or more fold compared to the expression level orthe function level of the component in the control sample. Any suitablemethods known in the art can be utilized to measure the expression levelor the function level of the component of the SWI/SNF complex. In someembodiments, the subject has malignant rhabdoid tumor, medulloblastomaor atypical teratoid rhabdoid tumor. In some embodiments, the componentis SNF5, ARID1A or ATRX.

For example, the identified subject can be treated with the standard ofcare treatment as described in the most current National ComprehensiveCancer Network (NCCN) guidelines.

For example, a control sample is obtained from a healthy, normalsubject. Alternatively, a control sample is obtained from a subject whois not suffering, has not been diagnosed, or is not at risk ofdeveloping cancer associated with the SWI/SNF complex.

In one preferred aspect, the present invention provides a method fortreating or alleviating a symptom of cancer in a subject by determiningresponsiveness of the subject to an EZH2 inhibitor and administering tothe subject a therapeutically effective amount of the EZH2 inhibitor ifthe subject is responsive to the EZH2 inhibitor and the subject has acancer selected from the group consisting of brain and CNS cancer,kidney cancer, ovarian cancer, pancreatic cancer, leukemia, lymphoma,myeloma, and/or sarcoma. Such responsiveness is determined by obtaininga sample from the subject and detecting reduced expression,haploinsufficiency, and/or loss of function of SNF5, ARID1A, and/orATRX, and the presence of the reduced expression, haploinsufficiency,and/or loss of function indicates the subject is responsive to the EZH2inhibitor.

In another preferred aspect, the present invention provides a method fortreating or alleviating a symptom of malignant rhabdoid tumor in asubject by determining responsiveness of the subject to an EZH2inhibitor and administering to the subject a therapeutically effectiveamount of the EZH2 inhibitor if the subject is responsive to the EZH2inhibitor. Such responsiveness is determined by obtaining a sample fromthe subject and detecting reduced expression, haploinsufficiency, and/orloss of function of SNF5, ARID1A, and/or ATRX, and the presence of thereduced expression, haploinsufficiency, and/or loss of functionindicates the subject is responsive to the EZH2 inhibitor.

In another preferred aspect, the present invention provides a method fortreating or alleviating a symptom of medulloblastoma in a subject bydetermining responsiveness of the subject to an EZH2 inhibitor andadministering to the subject a therapeutically effective amount of theEZH2 inhibitor if the subject is responsive to the EZH2 inhibitor. Suchresponsiveness is determined by obtaining a sample from the subject anddetecting reduced expression, haploinsufficiency, and/or loss offunction of SNF5, ARID1A, and/or ATRX, and the presence of the reducedexpression, haploinsufficiency, and/or loss of function indicates thesubject is responsive to the EZH2 inhibitor.

In another preferred aspect, the present invention provides a method fortreating or alleviating a symptom of atypical teratoid rhabdoid tumor ina subject by determining responsiveness of the subject to an EZH2inhibitor and administering to the subject a therapeutically effectiveamount of the EZH2 inhibitor if the subject is responsive to the EZH2inhibitor. Such responsiveness is determined by obtaining a sample fromthe subject and detecting reduced expression, haploinsufficiency, and/orloss of function of SNF5, ARID1A, and/or ATRX, and the presence of thereduced expression, haploinsufficiency, and/or loss of functionindicates the subject is responsive to the EZH2 inhibitor.

Malignant rhabdoid tumors (MRTs) and atypical teratoid rhabdoid tumors(ATRTs) are extremely aggressive pediatric cancers of the brain, kidney,and soft tissues that are highly malignant, locally invasive, frequentlymetastatic, and particularly lethal. They are typically diploid and lackgenomic aberrations; however, they are characterized by an almostcomplete penetrance of loss of SMARCB1 (also called SNF5, INI1 orBAF47), a core component of the SWI/SNF chromatin remodeling complex.The biallelic inactivation of SMARCB1 is in essence the sole geneticevent in MRTs and ATRTs which suggests a driver role for this geneticaberration.

Without being bound by any theory, a compound of the present inventionspecifically inhibits cellular H3K27 methylation leading to selectiveapoptotic killing of SMARCB1 mutant MRT cells. For example, in vitrotreatment of SMARCB1-deleted MRT cell lines with Compound A inducedstrong anti-proliferative effects with IC₅₀ values in the nM range;while the control (wild-type) cell lines were minimally affected (FIG.10C and table 6). Furthermore, the compound of the present inventioninduces genes of neuronal differentiation, cell cycle inhibition andtumor suppression while suppressing expression of hedgehog pathwaygenes, MYC and EZH2. For example, Compound A treatment of G401SMARCB1-deleted cells for up to 7 days strongly induced expression ofCD133, DOCK4 and PTPRK and up-regulated cell cycle inhibitors CDKN1A andCDKN2A and tumor suppressor BIN1, all in a time-dependent manner (FIG.14B). Simultaneously, the expression of hedgehog pathway genes, MYC andEZH2 were reduced. Notably, G402 SMARCB1-deleted cells exposed toCompound A for 14 days assumed a neuron-like morphology (FIG. 14C).

Accordingly, the present invention further provides methods of treatingor alleviating a symptom of cancer in a subject in need thereof by (a)determining the expression level of at least one gene selected from thegroup consisting of neuronal differentiation genes, cell cycleinhibition genes and tumor suppressor genes in a sample obtained fromthe subject; (b) selecting a subject having a decreased expression levelof at least one gene in step (a); and (c) administering to the subjectselected in step (b) an effective amount of a compound of the invention,thus treating or alleviating a symptom of cancer in the subject.

The present invention also provides methods of treating or alleviating asymptom of cancer in a subject in need thereof by (a) determining theexpression level of at least one gene selected from the group consistingof hedgehog pathway genes, myc pathway genes and histonemethyltransferase genes in a sample obtained from the subject; (b)selecting a subject having an increased expression level of at least onegene in step (a); and (c) administering to the subject selected in step(b) an effective amount of a compound of the invention, thus treating oralleviating a symptom of cancer in the subject.

Also provided herein are methods of selecting a cancer therapy for asubject in need thereof by (a) determining the expression level of atleast one gene selected from the group consisting of neuronaldifferentiation genes, cell cycle inhibition genes, and tumor suppressorgenes in a sample obtained from the subject, and (b) selecting a cancertherapy when the subject has a decreased expression level of at leastone gene in step (a), where the cancer therapy includes theadministration of an effective amount of a compound of the invention tothe subject.

The present invention further provides methods of selecting a cancertherapy for a subject in need thereof by (a) determining the expressionlevel of at least one gene selected from the group consisting ofhedgehog pathway genes, myc pathway genes and histone methyltransferasegenes in a sample obtained from the subject, and (b) selecting a cancertherapy when the subject has an increased expression level of at leastone gene in step (a), where the cancer therapy includes theadministration of an effective amount of a compound of the invention tothe subject.

In merely illustrative embodiments, the methods presented herein mayinclude the steps of (a) collecting a nucleic acid or a protein samplefrom a biological sample obtained from a subject, (b) measuring theexpression level of at least one gene selected from the group consistingof neuronal differentiation genes, cell cycle inhibition genes, andtumor suppressor genes in the sample, (c) measuring the expression levelof the same gene(s) in a control sample; (d) comparing the expressionlevel of the gene measured in step (b) in the tested sample to theexpression level of the gene measured in step (c) in the control sample(or to a reference value); (e) identifying the subject as a candidatefor treatment when the expression level of the component measured instep (b) is reduced compared to the expression level of the genemeasured in step (c); and (f) administering a therapeutically effectiveamount of an EZH2 inhibitor to the subject identified in step (e) orselecting a treatment regimen for the subject identified in step (e).The expression level of the gene in the tested subject is reduced, forexample, 10%, 25%, 50% or 1-, 2-, 5- or more fold compared to theexpression level of the gene in the control sample.

In merely illustrative embodiments, the methods presented herein mayinclude the steps of (a) collecting a nucleic acid or a protein samplefrom a biological sample obtained from a subject, (b) measuring theexpression level of at least one gene selected from the group consistingof hedgehog pathway genes, myc pathway genes and histonemethyltransferase genes in the sample, (c) measuring the expressionlevel of the same gene(s) in a control sample; (d) comparing theexpression level of the gene measured in step (b) in the tested sampleto the expression level of the gene measured in step (c) in the controlsample (or to a reference value); (e) identifying the subject as acandidate for treatment when the expression level of the componentmeasured in step (b) is increased compared to the expression level ofthe gene measured in step (c); and (f) administering a therapeuticallyeffective amount of an EZH2 inhibitor to the subject identified in step(e) or selecting a treatment regimen for the subject identified in step(e). The expression level of the gene in the tested subject isincreased, for example, 10%, 25%, 50% or 1-, 2-, 5- or more foldcompared to the expression level of the gene in the control sample.

The term “expression level” refers to protein, RNA, or mRNA level of aparticular gene of interest. Any methods known in the art can beutilized to determine the expression level of a particular gene ofinterest. Examples include, but are not limited to, reversetranscription and amplification assays (such as PCR, ligation RT-PCR orquantitative RT-PCT), hybridization assays, Northern blotting, dotblotting, in situ hybridization, gel electrophoresis, capillaryelectrophoresis, column chromatography, Western blotting,immunohistochemistry, immunostaining, or mass spectrometry. Assays canbe performed directly on biological samples or on protein/nucleic acidsisolated from the samples. It is routine practice in the relevant art tocarry out these assays. For example, the measuring step in any methoddescribed herein includes contacting the nucleic acid sample from thebiological sample obtained from the subject with one or more primersthat specifically hybridize to the gene of interest presented herein.Alternatively, the measuring step of any method described hereinincludes contacting the protein sample from the biological sampleobtained from the subject with one or more antibodies that bind to thebiomarker of the interest presented herein.

A decreased expression level of a particular gene means a decrease inits expression level by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%,400%, 500%, 1000%, 1500%, or more compared to a reference value or theexpression level of this gene measured in a different (or previous)sample obtained from the same subject.

An increased expression level of a particular gene means an increase inits expression level by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%,45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%,400%, 500%, 1000%, 1500%, or more compared to a reference value or theexpression level of this gene measured in a different (or previous)sample obtained from the same subject.

A “reference or baseline level/value” as used herein can be usedinterchangeably and is meant to be relative to a number or value derivedfrom population studies, including without limitation, such subjectshaving similar age range, disease status (e.g., stage), subjects in thesame or similar ethnic group, or relative to the starting sample of asubject undergoing treatment for cancer. Such reference values can bederived from statistical analyses and/or risk prediction data ofpopulations obtained from mathematical algorithms and computed indicesof cancer. Reference indices can also be constructed and used usingalgorithms and other methods of statistical and structuralclassification.

In some embodiments of the present invention, the reference or baselinevalue is the expression level of a particular gene of interest in acontrol sample derived from one or more healthy subjects or subjects whohave not been diagnosed with any cancer.

In some embodiments of the present invention, the reference or baselinevalue is the expression level of a particular gene of interest in asample obtained from the same subject prior to any cancer treatment. Inother embodiments of the present invention, the reference or baselinevalue is the expression level of a particular gene of interest in asample obtained from the same subject during a cancer treatment.Alternatively, the reference or baseline value is a prior measurement ofthe expression level of a particular gene of interest in a previouslyobtained sample from the same subject or from a subject having similarage range, disease status (e.g., stage) to the tested subject.

In some embodiments, an effective amount means an amount sufficient toincrease the expression level of at least one gene which is decreased inthe subject prior to the treatment or an amount sufficient to alleviateone or more symptoms of cancer. For example, an effective amount is anamount sufficient to increase the expression level of at least one geneselected from the group consisting of neuronal differentiation genes,cell cycle inhibition genes, and tumor suppressor genes by at least 5%,10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%,80%, 85%, 90%, 95%, 100%, 200%, 300%, 400%, 500%, 1000%, 1500%, or morecompared to a reference value or the expression level without thetreatment of any compound.

In some embodiments, an effective amount means an amount sufficient todecrease the expression level of at least one gene which is increased inthe subject prior to the treatment or an amount sufficient to alleviateone or more symptoms of cancer. For example, an effective amount is anamount sufficient to decrease the expression level of at least one geneselected from the group consisting of hedgehog pathway genes, MYC andEZH2 by at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%,60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%, 400%, 500%,1000%, 1500%, or more compared to a reference value or the expressionlevel without the treatment of any compound.

The precise effective amount for a subject will depend upon thesubject's body weight, size, and health; the nature and extent of thecondition; and the therapeutic selected for administration. An effectiveamount for a given situation can be determined by routineexperimentation that is within the skill and judgment of the clinician.

The present invention further provides a method of determining efficacyof a cancer treatment in a subject in need thereof by (a) measuring theexpression level of at least one gene selected from the group consistingof neuronal differentiation genes, cell cycle inhibition genes, andtumor suppressor genes in a sample obtained from the subject, (b)comparing the expression level of at least one gene in step (a) to areference value or a prior measurement, and (c) determining the efficacyof the cancer treatment based on the comparison step. An exemplarycancer treatment is administering a compound of the invention to thetested subject.

The treatment is effective when the tested subject has an increasedexpression of at least one gene selected from the group consisting ofneuronal differentiation genes, cell cycle inhibition genes and tumorsuppressor genes 1) compared to a reference value or a priormeasurement; or 2) over the period of time being monitored, such as 1,2, 3, 4, 5, 6, or 7 days, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 weeks, or 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months or longer. When the existingtreatment is not effective, a new treatment or an increased dosage ofthe existing treatment (for example, increasing the dosage of thecompound administered to the subject) should be sought for the testedsubject.

The present invention also provides a method of determining efficacy ofa cancer treatment in a subject in need thereof by (a) measuring theexpression level of at least one gene selected from the group consistingof hedgehog pathway genes, myc pathway genes and histonemethyltransferase genes in a sample obtained from the subject, (b)comparing the expression level of at least one gene in step (a) to areference value or a prior measurement, and (c) determining the efficacyof the cancer treatment based on the comparison step. An exemplarycancer treatment is administering an EZH2 inhibitor of the invention tothe tested subject.

For example, the treatment is effective when the tested subject has adecreased expression of at least one gene selected from the groupconsisting of hedgehog pathway genes, myc pathway genes and histonemethyltransferase genes 1) compared to a reference value or a priormeasurement; or 2) over the period of time being monitored, such as 1,2, 3, 4, 5, 6, or 7 days, or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 weeks, or 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months or longer. When the existingtreatment is not effective, a new treatment or an increased dosage ofthe existing treatment (for example, increasing the dosage of thecompound administered to the subject) should be sought for the testedsubject.

In any methods presented herein, cancer is selected from the groupconsisting of brain and central nervous system (CNS) cancer, head andneck cancer, kidney cancer, ovarian cancer, pancreatic cancer, leukemia,lung cancer, lymphoma, myeloma, sarcoma, breast cancer, and prostatecancer. Preferably, cancer is selected from the group consisting ofmedulloblastoma, oligodendroglioma, ovarian clear cell adenocarcinoma,ovarian endomethrioid adenocarcinoma, ovarian serous adenocarcinoma,pancreatic ductal adenocarcinoma, pancreatic endocrine tumor, malignantrhabdoid tumor, astrocytoma, atypical teratoid rhabdoid tumor, choroidplexus carcinoma, choroid plexus papilloma, ependymoma, glioblastoma,meningioma, neuroglial tumor, oligoastrocytoma, oligodendroglioma,pineoblastoma, carcinosarcoma, chordoma, extragonadal germ cell tumor,extrarenal rhabdoid tumor, schwannoma, skin squamous cell carcinoma,chondrosarcoma, clear cell sarcoma of soft tissue, ewing sarcoma,gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma,epithelioid sarcoma, renal medullo carcinoma, diffuse large B-celllymphoma, follicular lymphoma and not otherwise specified (NOS) sarcoma.More preferably, cancer is medulloblastoma, malignant rhabdoid tumor, oratypical teratoid rhabdoid tumor.

As used herein, the term “responsiveness” is interchangeable with terms“responsive”, “sensitive”, and “sensitivity”, and it is meant that asubject is showing therapeutic responses when administered an EZHinhibitor, e.g., tumor cells or tumor tissues of the subject undergoapoptosis and/or necrosis, and/or display reduced growing, dividing, orproliferation. This term is also meant that a subject will or has ahigher probability, relative to the population at large, of showingtherapeutic responses when administered an EZH inhibitor, e.g., tumorcells or tumor tissues of the subject undergo apoptosis and/or necrosis,and/or display reduced growing, dividing, or proliferation.

As used herein, a “subject” is interchangeable with a “subject in needthereof”, both of which refer to a subject having a disorder in whichEZH2-mediated protein methylation plays a part, or a subject having anincreased risk of developing such disorder relative to the population atlarge. A subject in need thereof may be a subject having a disorderassociated with SWI/SNF complex. A subject in need thereof can have aprecancerous condition. Preferably, a subject in need thereof hascancer. A subject in need thereof can have cancer associated withSWI/SNF complex. A subject in need thereof can have cancer associatedwith loss of function in at least one component of SWI/SNF complex. In apreferred aspect, a subject in need thereof has one or more cancersselected from the group consisting of brain and central nervous system(CNS) cancer, head and neck cancer, kidney cancer, ovarian cancer,pancreatic cancer, leukemia, lung cancer, lymphoma, myeloma, sarcoma,breast cancer, and prostate cancer. Preferably, a subject in needthereof has medulloblastoma, oligodendroglioma, ovarian clear celladenocarcinoma, ovarian endomethrioid adenocarcinoma, ovarian serousadenocarcinoma, pancreatic ductal adenocarcinoma, pancreatic endocrinetumor, malignant rhabdoid tumor, astrocytoma, atypical teratoid rhabdoidtumor, choroid plexus carcinoma, choroid plexus papilloma, ependymoma,glioblastoma, meningioma, neuroglial tumor, oligoastrocytoma,oligodendroglioma, pineoblastoma, carcinosarcoma, chordoma, extragonadalgerm cell tumor, extrarenal rhabdoid tumor, schwannoma, skin squamouscell carcinoma, chondrosarcoma, clear cell sarcoma of soft tissue, ewingsarcoma, gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma,epithelioid sarcoma, renal medullo carcinoma, diffuse large B-celllymphoma, follicular lymphoma and not otherwise specified (NOS) sarcoma.Alternatively, a subject in need thereof has a non NHL cancer.

As used herein, a “subject” includes a mammal. The mammal can be e.g., ahuman or appropriate non-human mammal, such as primate, mouse, rat, dog,cat, cow, horse, goat, camel, sheep or a pig. The subject can also be abird or fowl. In one embodiment, the mammal is a human. A subject can bemale or female.

A subject in need thereof can be one who has not been previouslydiagnosed or identified as having cancer or a precancerous condition. Asubject in need thereof can be one who has been previously diagnosed oridentified as having cancer or a precancerous condition. A subject inneed thereof can also be one who is having (suffering from) cancer or aprecancerous condition. Alternatively, a subject in need thereof can beone who has a risk of developing such disorder relative to thepopulation at large (i.e., a subject who is predisposed to developingsuch disorder relative to the population at large).

Optionally a subject in need thereof has already undergone, isundergoing or will undergo, at least one therapeutic intervention forthe cancer or precancerous condition.

A subject in need thereof may have refractory cancer on most recenttherapy. “Refractory cancer” means cancer that does not respond totreatment. The cancer may be resistant at the beginning of treatment orit may become resistant during treatment. Refractory cancer is alsocalled resistant cancer. In some embodiments, the subject in needthereof has cancer recurrence following remission on most recenttherapy. In some embodiments, the subject in need thereof received andfailed all known effective therapies for cancer treatment. In someembodiments, the subject in need thereof received at least one priortherapy.

A subject in need thereof may be one who had, is having or ispredisposed to developing a cancer or a precancerous conditionassociated with the SWI/SNF complex. A subject in need thereof may beone who had, is having or is predisposed to developing cancer or aprecancerous condition associated with loss of function of at least onecomponent of the SWI/SNF complex. In a preferred aspect, a subject inneed thereof is one who had, is having or is predisposed to developingone or more cancers selected from the group consisting of brain andcentral nervous system (CNS) cancer, head and neck cancer, kidneycancer, ovarian cancer, pancreatic cancer, leukemia, lung cancer,lymphoma, myeloma, sarcoma, breast cancer, and prostate cancer.Preferably, a subject in need thereof is one who had, is having or ispredisposed to developing brain and CNS cancer, kidney cancer, ovariancancer, pancreatic cancer, leukemia, lymphoma, myeloma, and/or sarcoma.Exemplary brain and central CNS cancer includes medulloblastoma,oligodendroglioma, atypical teratoid rhabdoid tumor, choroid plexuscarcinoma, choroid plexus papilloma, ependymoma, glioblastoma,meningioma, neuroglial tumor, oligoastrocytoma, oligodendroglioma, andpineoblastoma. Exemplary ovarian cancer includes ovarian clear celladenocarcinoma, ovarian endomethrioid adenocarcinoma, and ovarian serousadenocarcinoma. Exemplary pancreatic cancer includes pancreatic ductaladenocarcinoma and pancreatic endocrine tumor. Exemplary sarcomaincludes chondrosarcoma, clear cell sarcoma of soft tissue, ewingsarcoma, gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma,and not otherwise specified (NOS) sarcoma. Alternatively, cancers to betreated by the compounds of the present invention are non NHL cancers.

Alternatively, a subject in need thereof is one who had, is having or ispredisposed to developing one or more cancers selected from the groupconsisting of medulloblastoma, oligodendroglioma, ovarian clear celladenocarcinoma, ovarian endomethrioid adenocarcinoma, ovarian serousadenocarcinoma, pancreatic ductal adenocarcinoma, pancreatic endocrinetumor, malignant rhabdoid tumor, astrocytoma, atypical teratoid rhabdoidtumor, choroid plexus carcinoma, choroid plexus papilloma, ependymoma,glioblastoma, meningioma, neuroglial tumor, oligoastrocytoma,oligodendroglioma, pineoblastoma, carcinosarcoma, chordoma, extragonadalgerm cell tumor, extrarenal rhabdoid tumor, schwannoma, skin squamouscell carcinoma, chondrosarcoma, clear cell sarcoma of soft tissue, ewingsarcoma, gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma,and not otherwise specified (NOS) sarcoma. Preferably, a subject is onewho had, is having or is predisposed to developing medulloblastoma,ovarian clear cell adenocarcinoma, ovarian endomethrioid adenocarcinoma,pancreatic ductal adenocarcinoma, malignant rhabdoid tumor, atypicalteratoid rhabdoid tumor, choroid plexus carcinoma, choroid plexuspapilloma, glioblastoma, meningioma, pineoblastoma, carcinosarcoma,extrarenal rhabdoid tumor, schwannoma, skin squamous cell carcinoma,chondrosarcoma, ewing sarcoma, epithelioid sarcoma, renal medullocarcinoma, diffuse large B-cell lymphoma, follicular lymphoma and/or NOSsarcoma. More preferably, a subject in need thereof is one who had, ishaving or is predisposed to developing malignant rhabdoid tumor,medulloblastoma and/or atypical teratoid rhabdoid tumor.

In some embodiments of the present invention, a subject in need thereofhas a decreased expression level of at least one gene selected from thegroup consisting of neuronal differentiation genes, cell cycleinhibition genes, and tumor suppressor genes.

In some embodiments, a subject in need thereof has an increasedexpression level of at least one gene selected from the group consistingof hedgehog pathway genes, myc pathway genes and histonemethyltransferase genes.

In some embodiments of the present invention, a subject in need thereofhas loss of function of at least one component/subunit of the SWI/SNFcomplex. Alternatively, a subject in need thereof has reduced expressionor haploinsufficiency of at least one component/subunit of the SWI/SNFcomplex. In certain embodiments, a subject in need thereof has loss offunction of SNF5 subunit.

In any method of the present invention, a subject in need thereof mayhave reduced expression, haploinsufficiency or loss of function of atleast one signaling component downstream of SWI/SNF complex. Suchdownstream component includes, but is not limited to, polycomb complex(PcG) and its targets.

As used herein, the term “loss of function” refers to less or nofunction of a gene product/protein compared to the wild type. Loss offunction of a SWI/SNF complex component means the component/subunit orthe entire SWI/SNF complex has less or no biological function comparedto the wild type component/subunit or the entire SWI/SNF complex,respectively. Loss of function can be caused by transcriptional,post-transcription, or post translational mechanisms. In one aspect ofthe present invention, loss of function is caused by loss of functionmutation resulted from a point mutation (e.g., a substitution, amissense mutation, or a nonsense mutation), an insertion, and/or adeletion in a polypeptide of a SWI/SNF complex component or a nucleicacid sequence encoding a polypeptide of a SWI/SNF complex component. Themutations referred herein are somatic mutations. The term “somaticmutation” refers to a deleterious alteration in at least one gene allelethat is not found in every cell of the body, but is found only inisolated cells. A characteristic of the somatic mutations as used hereinis, that they are restricted to particular tissues or even parts oftissues or cells within a tissue and are not present in the wholeorganism harboring the tissues or cells. The term “wild-type” refers toa gene or gene product that has the characteristics of that gene or geneproduct when isolated from a naturally occurring source. A wild-typegene is that which is most frequently observed in a population and isthus arbitrarily designed the “normal” or “wild-type” form of the gene.

Accordingly, a loss of function mutation or a reduced expression can bedetected using any suitable method available in the art. For example, aloss of function mutation can be detected by measuring the biologicalfunction of a gene product, such as the ATP-dependent chromatinremodeling activity of the SWI/SNF complex. Alternatively, a loss offunction mutation can be determined by detecting any alternation in anucleic acid sequence encoding a component of the SWI/SNF complex. Forexample, a nucleic acid sequence encoding a component of the SWI/SNFcomplex having a loss of function mutation can be detected bywhole-genome resequencing or target region resequencing (the latter alsoknown as targeted resequencing) using suitably selected sources of DNAand polymerase chain reaction (PCR) primers in accordance with methodswell known in the art. The method typically and generally entails thesteps of genomic DNA purification, PCR amplification to amplify theregion of interest, cycle sequencing, sequencing reaction cleanup,capillary electrophoresis, and/or data analysis. Alternatively or inaddition, the method may include the use of microarray-based targetedregion genomic DNA capture and/or sequencing. Kits, reagents, andmethods for selecting appropriate PCR primers and performingresequencing are commercially available, for example, from AppliedBiosystems, Agilent, and NimbleGen (Roche Diagnostics GmbH).Alternatively or in addition, a nucleic acid sequence encoding a SWI/SNFpolypeptide having a loss of function mutation may be detected using aSouthern blot in accordance with methods well known in the art.Optionally, a loss of function mutation can be detected by measuring theabsence of the expression of a component polypeptide or by measuring theexpression of the mutant component polypeptide. Detection of (mutant)polypeptide expression can be carried out with any suitable immunoassayin the art, such as Western blot analysis.

Human nucleic acid and amino acid sequence of components of the SWI/SNFcomplex have previously been described. See, e.g., GenBank Accession NosNP_003064.2, NM_003073.3, NP_001007469.1, and NM_001007468.1 for SNF5,GenBank Accession Nos NM_000489.3, NP_000480.2, NM_138270.2, andNP_612114.1 for ATRX, GenBank Accession Nos NP_006006.3, NM_006015.4,NP_624361.1, and NM_139135.2 for ARID1A, each of which is incorporatedherein by reference in its entirety.

Spectrum of hSNF5 somatic mutations in human has also been described inSevenet et al., Human Molecular Genetics, 8: 2359-2368, 1999, which isincorporated herein by reference in its entirety.

A subject in need thereof may have reduced expression,haploinsufficiency, and/or loss of function of SNF5. For example, asubject can comprise a deletion of SNF5 in SNF5 polypeptide or a nucleicacid sequence encoding a SNF5 polypeptide.

SWI/SNF-related matrix-associated actin-dependent regulator of chromatinsubfamily B member 1 isoform a (SMARCB1, also called SNF5) [Homo sapiens](SEQ ID NO: 1)    1mmmmalsktf gqkpvkfqle ddgefymigs evgnylrmfr gslykrypsl wrrlatveer   61kkivasshgk ktkpntkdhg yttlatsvtl lkaseveeil dgndekykav sistepptyl  121reqkakrnsq wvptlpnssh hldavpcstt inrnrmgrdk krtfplcfdd hdpavihena  181sqpevlvpir ldmeidgqkl rdaftwnmne klmtpemfse ilcddldlnp ltfvpaiasa  241irqqiesypt dsiledqsdq rviiklnihv gnislvdqfe wdmsekensp ekfalklcse  301lglggefvtt iaysirgqls whqktyafse nplptveiai rntgdadqwc plletltdae  361mekkirdqdr ntrrmrrlan tapawHomo sapiens SWI/SNF related, matrix associated, actin dependentregulator of chromatin, subfamily b, member 1 (SMARCB1, also calledSNF5), transcript variant 1, mRNA (SEQ ID NO: 2)    1aacgccagcg cctgcgcact gagggcggcc tggtcgtcgt ctgcggcggc ggcggcggct   61gaggagcccg gctgaggcgc cagtacccgg cccggtccgc atttcgcctt ccggcttcgg  121tttccctcgg cccagcacgc cccggccccg ccccagccct cctgatccct cgcagcccgg  181ctccggccgc ccgcctctgc cgccgcaatg atgatgatgg cgctgagcaa gaccttcggg  241cagaagcccg tgaagttcca gctggaggac gacggcgagt tctacatgat cggctccgag  301gtgggaaact acctccgtat gttccgaggt tctctgtaca agagataccc ctcactctgg  361aggcgactag ccactgtgga agagaggaag aaaatagttg catcgtcaca tggtaaaaaa  421acaaaaccta acactaagga tcacggatac acgactctag ccaccagtgt gaccctgtta  481aaagcctcgg aagtggaaga gattctggat ggcaacgatg agaagtacaa ggctgtgtcc  541atcagcacag agccccccac ctacctcagg gaacagaagg ccaagaggaa cagccagtgg  601gtacccaccc tgcccaacag ctcccaccac ttagatgccg tgccatgctc cacaaccatc  661aacaggaacc gcatgggccg agacaagaag agaaccttcc ccctttgctt tgatgaccat  721gacccagctg tgatccatga gaacgcatct cagcccgagg tgctggtccc catccggctg  781gacatggaga tcgatgggca gaagctgcga gacgccttca cctggaacat gaatgagaag  841ttgatgacgc ctgagatgtt ttcagaaatc ctctgtgacg atctggattt gaacccgctg  901acgtttgtgc cagccatcgc ctctgccatc agacagcaga tcgagtccta ccccacggac  961agcatcctgg aggaccagtc agaccagcgc gtcatcatca agctgaacat ccatgtggga 1021aacatttccc tggtggacca gtttgagtgg gacatgtcag agaaggagaa ctcaccagag 1081aagtttgccc tgaagctgtg ctcggagctg gggttgggcg gggagtttgt caccaccatc 1141gcatacagca tccggggaca gctgagctgg catcagaaga cctacgcctt cagcgagaac 1201cctctgccca cagtggagat tgccatccgg aacacgggcg atgcggacca gtggtgccca 1261ctgctggaga ctctgacaga cgctgagatg gagaagaaga tccgcgacca ggacaggaac 1321acgaggcgga tgaggcgtct tgccaacacg gccccggcct ggtaaccagc ccatcagcac 1381acggctccca cggagcatct cagaagattg ggccgcctct cctccatctt ctggcaagga 1441cagaggcgag gggacagccc agcgccatcc tgaggatcgg gtgggggtgg agtgggggct 1501tccaggtggc ccttcccggc acacattcca tttgttgagc cccagtcctg ccccccaccc 1561caccctccct acccctcccc agtctctggg gtcaggaaga aaccttattt taggttgtgt 1621tttgtttttg tataggagcc ccaggcaggg ctagtaacag tttttaaata aaaggcaaca 1681ggtcatgttc aatttcttca acaaaaaaaa aaaaaaaSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 isoform b [Homo sapiens] (SMARCB1,also called SNF5) (SEQ ID NO: 3)    1mmmmalsktf gqkpvkfqle ddgefymigs evgnylrmfr gslykrypsl wrrlatveer   61kkivasshdh gyttlatsvt llkaseveei ldgndekyka vsisteppty lreqkakrns  121qwvptlpnss hhldavpcst tinrnrmgrd kkrtfplcfd dhdpavihen asqpevlvpi  181rldmeidgqk lrdaftwnmn eklmtpemfs eilcddldln pltfvpaias airqqiesyp  241tdsiledqsd qrviiklnih vgnislvdqf ewdmsekens pekfalklcs elglggefvt  301tiaysirgql swhqktyafs enplptveia irntgdadqw cplletltda emekkirdqd  361rntrrmrrla ntapawHomo sapiens SWI/SNF related, matrix associated, actin dependentregulator of chromatin, subfamily b, member 1 (SMARCB1, also calledSNF5), transcript variant 2, mRNA (SEQ ID NO: 4)    1aacgccagcg cctgcgcact gagggcggcc tggtcgtcgt ctgcggcggc ggcggcggct   61gaggagcccg gctgaggcgc cagtacccgg cccggtccgc atttcgcctt ccggcttcgg  121tttccctcgg cccagcacgc cccggccccg ccccagccct cctgatccct cgcagcccgg  181ctccggccgc ccgcctctgc cgccgcaatg atgatgatgg cgctgagcaa gaccttcggg  241cagaagcccg tgaagttcca gctggaggac gacggcgagt tctacatgat cggctccgag  301gtgggaaact acctccgtat gttccgaggt tctctgtaca agagataccc ctcactctgg  361aggcgactag ccactgtgga agagaggaag aaaatagttg catcgtcaca tgatcacgga  421tacacgactc tagccaccag tgtgaccctg ttaaaagcct cggaagtgga agagattctg  481gatggcaacg atgagaagta caaggctgtg tccatcagca cagagccccc cacctacctc  541agggaacaga aggccaagag gaacagccag tgggtaccca ccctgcccaa cagctcccac  601cacttagatg ccgtgccatg ctccacaacc atcaacagga accgcatggg ccgagacaag  661aagagaacct tccccctttg ctttgatgac catgacccag ctgtgatcca tgagaacgca  721tctcagcccg aggtgctggt ccccatccgg ctggacatgg agatcgatgg gcagaagctg  781cgagacgcct tcacctggaa catgaatgag aagttgatga cgcctgagat gttttcagaa  841atcctctgtg acgatctgga tttgaacccg ctgacgtttg tgccagccat cgcctctgcc  901atcagacagc agatcgagtc ctaccccacg gacagcatcc tggaggacca gtcagaccag  961cgcgtcatca tcaagctgaa catccatgtg ggaaacattt ccctggtgga ccagtttgag 1021tgggacatgt cagagaagga gaactcacca gagaagtttg ccctgaagct gtgctcggag 1081ctggggttgg gcggggagtt tgtcaccacc atcgcataca gcatccgggg acagctgagc 1141tggcatcaga agacctacgc cttcagcgag aaccctctgc ccacagtgga gattgccatc 1201cggaacacgg gcgatgcgga ccagtggtgc ccactgctgg agactctgac agacgctgag 1261atggagaaga agatccgcga ccaggacagg aacacgaggc ggatgaggcg tcttgccaac 1321acggccccgg cctggtaacc agcccatcag cacacggctc ccacggagca tctcagaaga 1381ttgggccgcc tctcctccat cttctggcaa ggacagaggc gaggggacag cccagcgcca 1441tcctgaggat cgggtggggg tggagtgggg gcttccaggt ggcccttccc ggcacacatt 1501ccatttgttg agccccagtc ctgcccccca ccccaccctc cctacccctc cccagtctct 1561ggggtcagga agaaacctta ttttaggttg tgttttgttt ttgtatagga gccccaggca 1621gggctagtaa cagtttttaa ataaaaggca acaggtcatg ttcaatttct tcaacaaaaa 1681aaaaaaaaaa

A subject in need thereof may have reduced expression,haploinsufficiency, and/or loss of function of ATRX. For example, asubject can comprise a mutation selected from the group consisting of asubstitution of asparagine (N) for the wild type residue lysine (K) atamino acid position 688 of SEQ ID NO: 5 (K688N), and a substitution ofisoleucine (I) for the wild type residue methionine (M) at amino acidposition 366 of SEQ ID NO: 5 (M366I).

Homo sapiens alpha thalassemia/mental retardation syndrome X-linked(ATRX) isoform 1 (SEQ ID NO: 5)     1mtaepmsesk lntlvqklhd flahsseese etsspprlam nqntdkisgs gsnsdmmens    61keegtsssek skssgssrsk rkpsivtkyv esddekpldd etvnedasne nsenditmqs   121lpkgtvivqp epvlnedkdd fkgpefrsrs kmktenlkkr gedglhgivs ctacgqqvnh   181fqkdsiyrhp slqvlicknc fkyymsddis rdsdgmdeqc rwcaeggnli ccdfchnafc   241kkcilrnlgr kelstimden nqwycyichp eplldlvtac nsvfenleql lqqnkkkikv   301dseksnkvye htsrfspkkt ssncngeekk lddscsgsvt ysysalivpk emikkakkli   361ettanmnssy vkflkqatdn seissatklr qlkafksvla dikkahlale edlnsefram   421davnkekntk ehkvidakfe tkarkgekpc alekkdisks eaklsrkqvd sehmhqnvpt   481eeqrtnkstg gehkksdrke epqyepants edldmdivsv pssvpedife nletamevqs   541svdhqgdgss gteqevesss vklnisskdn rggiksktta kvtkelyvkl tpvslsnspi   601kgadcqevpq dkdgykscgl npklekcglg qensdnehlv enevslllee sdlrrsprvk   661ttplrrptet npvtsnsdee cnetvkekqk lsvpvrkkdk rnssdsaidn pkpnklpksk   721qsetvdqnsd sdemlailke vsrmshssss dtdineihtn hktlydlktq agkddkgkrk   781rksstsgsdf dtkkgksaks siiskkkrqt qsessnydse lekeiksmsk igaarttkkr   841ipntkdfdss edekhskkgm dnqghknlkt sqegssddae rkqeretfss aegtvdkdtt   901imelrdrlpk kqqasastdg vdklsgkeqs ftslevrkva etkekskhlk tktckkvgdg   961lsdiaekflk kdqsdetsed dkkqskkgte ekkkpsdfkk kvikmeqqye sssdgteklp  1021ereeichfpk gikqikngtt dgekkskkir dktskkkdel sdyaekstgk gdscdssedk  1081kskngaygre kkrckllgks srkrqdcsss dtekysmked gcnssdkrlk rielrerrnl  1141sskrntkeiq sgssssdaee ssednkkkkq rtsskkkavi vkekkrnslr tstkrkqadi  1201tsssssdied ddqnsigegs sdeqkikpvt enlvlsshtg fcgssgdeal sksvpvtvdd  1261ddddndpenr iakkmlleei kanlssdedg ssddepeegk krtgkqneen pgdeeaknqv  1321nsesdsdsee skkpryrhrl lrhkltvsdg esgeekktkp kehkevkgrn rrkvssedse  1381dsdfqesgvs eevsesedeq rprtrsakka eleenqrsyk qkkkrrrikv qedsssenks  1441nseeeeeeke eeeeeeeeee eeeedendds kspgkgrkki rkilkddklr tetqnalkee  1501eerrkriaer erereklrev ieiedasptk cpittklvld edeetkeplv qvhrnmvikl  1561kphqvdgvqf mwdcccesvk ktkkspgsgc ilahcmglgk tlqvvsflht vllcdkldfs  1621talvvcpint alnwmnefek wqeglkddek levselatvk rpgersymlq rwqedggvmi  1681igyemyrnla qgrnvksrkl keifnkalvd pgpdfvvcde ghilkneasa vskamnsirs  1741rrriiltgtp lqnnlieyhc mvnfikenll gsikefrnrf inpiqngqca dstmvdvrvm  1801kkrahilyem lagcvqrkdy taltkflppk heyvlavrmt siqcklyqyy ldhltgvgnn  1861seggrgkaga klfqdfqmls riwthpwclq ldyiskenkg yfdedsmdef iasdsdetsm  1921slssddytkk kkkgkkgkkd ssssgsgsdn dvevikvwns rsrgggegnv detgnnpsys  1981lkleeskats ssnpsspapd wykdfvtdad aevlehsgkm vllfeilrma eeigdkvlvf  2041sqslisldli edflelasre ktedkdkpli ykgegkwlrn idyyrldgst taqsrkkwae  2101efndetnvrg rlfiistkag slginlvaan rviifdaswn psydigsifr vyrfgqtkpv  2161yvyrflaqgt medkiydrqv tkqslsfrvv dqqqverhft mneltelytf epdllddpns  2221ekkkkrdtpm lpkdtilael lqihkehivg yhehdslldh keeeelteee rkaawaeyea  2281ekkgltmrfn iptgtnlppv sfnsqtpyip fnlgalsams nqqledlinq grekvveatn  2341svtavriqpl ediisavwke nmnlseaqvq alalsrqasq eldvkrreai yndvltkqqm  2401liscvqrilm nrrlqqqynq qqqqqmtyqq atlghlmmpk ppnlimnpsn yqqidmrgmy  2461qpvaggmqpp plqrapppmr sknpgpsqgk smHomo sapiens alpha thalassemia/mental retardation syndrome X-linked(ATRX), transcript variant 1, mRNA (SEQ ID NO: 6)     1aattctcctg cctgagcctc ggcccaacaa aatggcggcg gcagcggtgt cgctttgttt    61ccgcggctcc tgcggcggtg gcagtggtag cggcctttga gctgtgggga ggttccagca   121gcagctacag tgacgactaa gactccagtg catttctatc gtaaccgggc gcgggggagc   181gcagatcggc gcccagcaat cacagaagcc gacaaggcgt tcaagcgaaa acatgaccgc   241tgagcccatg agtgaaagca agttgaatac attggtgcag aagcttcatg acttccttgc   301acactcatca gaagaatctg aagaaacaag ttctcctcca cgacttgcaa tgaatcaaaa   361cacagataaa atcagtggtt ctggaagtaa ctctgatatg atggaaaaca gcaaggaaga   421gggaactagc tcttcagaaa aatccaagtc ttcaggatcg tcacgatcaa agaggaaacc   481ttcaattgta acaaagtatg tagaatcaga tgatgaaaaa cctttggatg atgaaactgt   541aaatgaagat gcgtctaatg aaaattcaga aaatgatatt actatgcaga gcttgccaaa   601aggtacagtg attgtacagc cagagccagt gctgaatgaa gacaaagatg attttaaagg   661gcctgaattt agaagcagaa gtaaaatgaa aactgaaaat ctcaaaaaac gcggagaaga   721tgggcttcat gggattgtga gctgcactgc ttgtggacaa caggtcaatc attttcaaaa   781agattccatt tatagacacc cttcattgca agttcttatt tgtaagaatt gctttaagta   841ttacatgagt gatgatatta gccgtgactc agatggaatg gatgaacaat gtaggtggtg   901tgcggaaggt ggaaacttga tttgttgtga cttttgccat aatgctttct gcaagaaatg   961cattctacgc aaccttggtc gaaaggagtt gtccacaata atggatgaaa acaaccaatg  1021gtattgctac atttgtcacc cagagccttt gttggacttg gtcactgcat gtaacagcgt  1081atttgagaat ttagaacagt tgttgcagca aaataagaag aagataaaag ttgacagtga  1141aaagagtaat aaagtatatg aacatacatc cagattttct ccaaagaaga ctagttcaaa  1201ttgtaatgga gaagaaaaga aattagatga ttcctgttct ggctctgtaa cctactctta  1261ttccgcacta attgtgccca aagagatgat taagaaggca aaaaaactga ttgagaccac  1321agccaacatg aactccagtt atgttaaatt tttaaagcag gcaacagata attcagaaat  1381cagttctgct acaaaattac gtcagcttaa ggcttttaag tctgtgttgg ctgatattaa  1441gaaggctcat cttgcattgg aagaagactt aaattccgag tttcgagcga tggatgctgt  1501aaacaaagag aaaaatacca aagagcataa agtcatagat gctaagtttg aaacaaaagc  1561acgaaaagga gaaaaacctt gtgctttgga aaagaaggat atttcaaagt cagaagctaa  1621actttcaaga aaacaggtag atagtgagca catgcatcag aatgttccaa cagaggaaca  1681aagaacaaat aaaagtaccg gtggtgaaca taagaaatct gatagaaaag aagaacctca  1741atatgaacct gccaacactt ctgaagattt agacatggat attgtgtctg ttccttcctc  1801agttccagaa gacatttttg agaatcttga gactgctatg gaagttcaga gttcagttga  1861tcatcaaggg gatggcagca gtggaactga acaagaagtg gagagttcat ctgtaaaatt  1921aaatatttct tcaaaagaca acagaggagg tattaaatca aaaactacag ctaaagtaac  1981aaaagaatta tatgttaaac tcactcctgt ttccctttct aattccccaa ttaaaggtgc  2041tgattgtcag gaagttccac aagataaaga tggctataaa agttgtggtc tgaaccccaa  2101gttagagaaa tgtggacttg gacaggaaaa cagtgataat gagcatttgg ttgaaaatga  2161agtttcatta cttttagagg aatctgatct tcgaagatcc ccacgtgtaa agactacacc  2221cttgaggcga ccgacagaaa ctaaccctgt aacatctaat tcagatgaag aatgtaatga  2281aacagttaag gagaaacaaa aactatcagt tccagtgaga aaaaaggata agcgtaattc  2341ttctgacagt gctatagata atcctaagcc taataaattg ccaaaatcta agcaatcaga  2401gactgtggat caaaattcag attctgatga aatgctagca atcctcaaag aggtgagcag  2461gatgagtcac agttcttctt cagatactga tattaatgaa attcatacaa accataagac  2521tttgtatgat ttaaagactc aggcggggaa agatgataaa ggaaaaagga aacgaaaaag  2581ttctacatct ggctcagatt ttgatactaa aaagggcaaa tcagctaaga gctctataat  2641ttctaaaaag aaacgacaaa cccagtctga gtcttctaat tatgactcag aattagaaaa  2701agagataaag agcatgagta aaattggtgc tgccagaacc accaaaaaaa gaattccaaa  2761tacaaaagat tttgactctt ctgaagatga gaaacacagc aaaaaaggaa tggataatca  2821agggcacaaa aatttgaaga cctcacaaga aggatcatct gatgatgctg aaagaaaaca  2881agagagagag actttctctt cagcagaagg cacagttgat aaagacacga ccatcatgga  2941attaagagat cgacttccta agaagcagca agcaagtgct tccactgatg gtgtcgataa  3001gctttctggg aaagagcaga gttttacttc tttggaagtt agaaaagttg ctgaaactaa  3061agaaaagagc aagcatctca aaaccaaaac atgtaaaaaa gtacaggatg gcttatctga  3121tattgcagag aaattcctaa agaaagacca gagcgatgaa acttctgaag atgataaaaa  3181gcagagcaaa aagggaactg aagaaaaaaa gaaaccttca gactttaaga aaaaagtaat  3241taaaatggaa caacagtatg aatcttcatc tgatggcact gaaaagttac ctgagcgaga  3301agaaatttgt cattttccta agggcataaa acaaattaag aatggaacaa ctgatggaga  3361aaagaaaagt aaaaaaataa gagataaaac ttctaaaaag aaggatgaat tatctgatta  3421tgctgagaag tcaacaggga aaggagatag ttgtgactct tcagaggata aaaagagtaa  3481gaatggagca tatggtagag agaagaaaag gtgcaagttg cttggaaaga gttcaaggaa  3541gagacaagat tgttcatcat ctgatactga gaaatattcc atgaaagaag atggttgtaa  3601ctcttctgat aagagactga aaagaataga attgagggaa agaagaaatt taagttcaaa  3661gagaaatact aaggaaatac aaagtggctc atcatcatct gatgctgagg aaagttctga  3721agataataaa aagaagaagc aaagaacttc atctaaaaag aaggcagtca ttgtcaagga  3781gaaaaagaga aactccctaa gaacaagcac taaaaggaag caagctgaca ttacatcctc  3841atcttcttct gatatagaag atgatgatca gaattctata ggtgagggaa gcagcgatga  3901acagaaaatt aagcctgtga ctgaaaattt agtgctgtct tcacatactg gattttgcca  3961atcttcagga gatgaagcct tatctaaatc agtgcctgtc acagtggatg atgatgatga  4021cgacaatgat cctgagaata gaattgccaa gaagatgctt ttagaagaaa ttaaagccaa  4081tctttcctct gatgaggatg gatcttcaga tgatgagcca gaagaaggga aaaaaagaac  4141tggaaaacaa aatgaagaaa acccaggaga tgaggaagca aaaaatcaag tcaattctga  4201atcagattca gattctgaag aatctaagaa gccaagatac agacataggc ttttgcggca  4261caaattgact gtgagtgacg gagaatctgg agaagaaaaa aagacaaagc ctaaagagca  4321taaagaagtc aaaggcagaa acagaagaaa ggtgagcagt gaagattcag aagattctga  4381ttttcaggaa tcaggagtta gtgaagaagt tagtgaatcc gaagatgaac agcggcccag  4441aacaaggtct gcaaagaaag cagagttgga agaaaatcag cggagctata aacagaaaaa  4501gaaaaggcga cgtattaagg ttcaagaaga ttcatccagt gaaaacaaga gtaattctga  4561ggaagaagag gaggaaaaag aagaggagga ggaagaggag gaggaggagg aagaggagga  4621ggaagatgaa aatgatgatt ccaagtctcc tggaaaaggc agaaagaaaa ttcggaagat  4681tcttaaagat gataaactga gaacagaaac acaaaatgct cttaaggaag aggaagagag  4741acgaaaacgt attgctgaga gggagcgtga gcgagaaaaa ttgagagagg tgatagaaat  4801tgaagatgct tcacccacca agtgtccaat aacaaccaag ttggttttag atgaagatga  4861agaaaccaaa gaacctttag tgcaggttca tagaaatatg gttatcaaat tgaaacccca  4921tcaagtagat ggtgttcagt ttatgtggga ttgctgctgt gagtctgtga aaaaaacaaa  4981gaaatctcca ggttcaggat gcattcttgc ccactgtatg ggccttggta agactttaca  5041ggtggtaagt tttcttcata cagttctttt gtgtgacaaa ctggatttca gcacggcgtt  5101agtggtttgt cctcttaata ctgctttgaa ttggatgaat gaatttgaga agtggcaaga  5161gggattaaaa gatgatgaga agcttgaggt ttctgaatta gcaactgtga aacgtcctca  5221ggagagaagc tacatgctgc agaggtggca agaagatggt ggtgttatga tcataggcta  5281tgagatgtat agaaatcttg ctcaaggaag gaatgtgaag agtcggaaac ttaaagaaat  5341atttaacaaa gctttggttg atccaggccc tgattttgtt gtttgtgatg aaggccatat  5401tctaaaaaat gaagcatctg ctgtttctaa agctatgaat tctatacgat caaggaggag  5461gattatttta acaggaacac cacttcaaaa taacctaatt gagtatcatt gtatggttaa  5521ttttatcaag gaaaatttac ttggatccat taaggagttc aggaatagat ttataaatcc  5581aattcaaaat ggtcagtgtg cagattctac catggtagat gtcagagtga tgaaaaaacg  5641tgctcacatt ctctatgaga tgttagctgg atgtgttcag aggaaagatt atacagcatt  5701aacaaaattc ttgcctccaa aacacgaata tgtgttagct gtgagaatga cttctattca  5761gtgcaagctc tatcagtact acttagatca cttaacaggt gtgggcaata atagtgaagg  5821tggaagagga aaggcaggtg caaagctttt ccaagatttt cagatgttaa gtagaatatg  5881gactcatcct tggtgtttgc agctagacta cattagcaaa gaaaataagg gttattttga  5941tgaagacagt atggatgaat ttatagcctc agattctgat gaaacctcca tgagtttaag  6001ctccgatgat tatacaaaaa agaagaaaaa agggaaaaag gggaaaaaag atagtagctc  6061aagtggaagt ggcagtgaca atgatgttga agtgattaag gtctggaatt caagatctcg  6121gggaggtggt gaaggaaatg tggatgaaac aggaaacaat ccttctgttt ctttaaaact  6181ggaagaaagt aaagctactt cttcttctaa tccaagcagc ccagctccag actggtacaa  6241agattttgtt acagatgctg atgctgaggt tttagagcat tctgggaaaa tggtacttct  6301ctttgaaatt cttcgaatgg cagaggaaat tggggataaa gtccttgttt tcagccagtc  6361cctcatatct ctggacttga ttgaagattt tcttgaatta gctagtaggg agaagacaga  6421agataaagat aaacccctta tttataaagg tgaggggaag tggcttcgaa acattgacta  6481ttaccgttta gatggttcca ctactgcaca gtcaaggaag aagtgggctg aagaatttaa  6541tgatgaaact aatgtgagag gacgattatt tatcatttct actaaagcag gatctctagg  6601aattaatctg gtagctgcta atcgagtaat tatattcgac gcttcttgga atccatctta  6661tgacatccag agtatattca gagtttatcg ctttggacaa actaagcctg tttatgtata  6721taggttctta gctcagggaa ccatggaaga taagatttat gatcggcaag taactaagca  6781gtcactgtct tttcgagttg ttgatcagca gcaggtggag cgtcatttta ctatgaatga  6841gcttactgaa ctttatactt ttgagccaga cttattagat gaccctaatt cagaaaagaa  6901gaagaagagg gatactccca tgctgccaaa ggataccata cttgcagagc tccttcagat  6961acataaagaa cacattgtag gataccatga acatgattct cttttggacc acaaagaaga  7021agaagagttg actgaagaag aaagaaaagc agcttgggct gagtatgaag cagagaagaa  7081gggactgacc atgcgtttca acataccaac tgggaccaat ttaccccctg tcagtttcaa  7141ctctcaaact ccttatattc ctttcaattt gggagccctg tcagcaatga gtaatcaaca  7201gctggaggac ctcattaatc aaggaagaga aaaagttgta gaagcaacaa acagtgtgac  7261agcagtgagg attcaacctc ttgaggatat aatttcagct gtatggaagg agaacatgaa  7321tctctcagag gcccaagtac aggcgttagc attaagtaga caagccagcc aggagcttga  7381tgttaaacga agagaagcaa tctacaatga tgtattgaca aaacaacaga tgttaatcag  7441ctgtgttcag cgaatactta tgaacagaag gctccagcag cagtacaatc agcagcaaca  7501gcaacaaatg acttatcaac aagcaacact gggtcacctc atgatgccaa agcccccaaa  7561tttgatcatg aatccttcta actaccagca gattgatatg agaggaatgt atcagccagt  7621ggctggtggt atgcagccac caccattaca gcgtgcacca cccccaatga gaagcaaaaa  7681tccaggacct tcccaaggga aatcaatgtg attttgcact aaaagcttaa tggattgtta  7741aaatcataga aagatctttt atttttttag gaatcaatga cttaacagaa ctcaactgta  7801taaatagttt ggtcccctta aatgccaatc ttccatatta gttttacttt tttttttttt  7861aaatagggca taccatttct tcctgacatt tgtcagtgat gttgcctaga atcttcttac  7921acacgctgag tacagaagat atttcaaatt gttttcagtg aaaacaagtc cttccataat  7981agtaacaact ccacagattt cctctctaaa tttttatgcc tgcttttagc aaccataaaa  8041ttgtcataaa attaataaat ttaggaaaga ataaagattt atatattcat tctttacata  8101taaaaacaca cagctgagtt cttagagttg attcctcaag ttatgaaata cttttgtact  8161taatccattt cttgattaaa gtgattgaaa tggttttaat gttcttttga ctgaagtctg  8221aaactgggct cctgctttat tgtctctgtg actgaaagtt agaaactgag ggttatcttt  8281gacacagaat tgtgtgcaat attcttaaat actactgctc taaaagttgg agaagtcttg  8341cagttatctt agcattgtat aaacagcctt aagtatagcc taagaagaga attccttttt  8401cttctttagt ccttctgcca ttttttattt tcagttatat gtgctgaaat aattactggt  8461aaaatttcag ggttgtggat tatcttccac acatgaattt tctctctcct ggcacgaata  8521taaagcacat ctcttaactg catggtgcca gtgctaatgc ttcatcctgt tgctggcagt  8581gggatgtgga cttagaaaat caagttctag cattttagta ggttaacact gaagttgtgg  8641ttgttaggtt cacaccctgt tttataaaca acatcaaaat ggcagaacca ttgctgactt  8701taggttcaca tgaggaatgt acttttaaca attcccagta ctatcagtat tgtgaaataa  8761ttcctctgaa agataagaat cactggcttc tatgcgcttc ttttctctca tcatcatgtt  8821cttttacccc agtttcctta cattttttta aattgtttca gagtttgttt tttttttagt  8881ttagattgtg aggcaattat taaatcaaaa ttaattcatc caatacccct ttactagaag  8941ttttactaga aaatgtatta cattttattt tttcttaatc cagttctgca aaaatgacct  9001ataaatttat tcatgtacaa ttttggttac ttgaattgtt aaagaaaaca ttgtttttga  9061ctatgggagt caactcaaca tggcagaacc atttttgaga tgatgataca acaggtagtg  9121aaacagctta agaattccaa aaaaaaaaaa aaaaaaaaaa aaaagaaaac tgggtttggg  9181ctttgcttta ggtatcactg gattagaatg agtttaacat tagctaaaac tgctttgagt  9241tgtttggatg attaagagat tgccattttt atcttggaag aactagtggt aaaacatcca  9301agagcactag gattgtgata cagaatttgt gaggtttggt ggatccacgc ccctctcccc  9361cactttccca tgatgaaata tcactaataa atcctgtata tttagatatt atgctagcca  9421tgtaatcaga tttatttaat tgggtggggc aggtgtgtat ttactttaga aaaaatgaaa  9481aagacaagat ttatgagaaa tatttgaagg cagtacactc tggccaactg ttaccagttg  9541gtatttctac aagttcagaa tattttaaac ctgatttact agacctggga attttcaaca  9601tggtctaatt atttactcaa agacatagat gtgaaaattt taggcaacct tctaaatctt  9661tttcaccatg gatgaaacta taacttaaag aataatactt agaagggtta attggaaatc  9721agagtttgaa ataaaacttg gaccactttg tatacactct tctcacttga cattttagct  9781atataatatg tactttgagt ataacatcaa gctttaacaa atatttaaag acaaaaaaat  9841cacgtcagta aaatactaaa aggctcattt ttatatttgt tttagatgtt ttaaatagtt  9901gcaatggatt aaaaatgatg atttaaaatg ttgcttgtaa tacagttttg cctgctaaat  9961tctccacatt ttgtaacctg ttttatttct ttgggtgtaa agcgtttttg cttagtattg 10021tgatattgta tatgttttgt cccagttgta tagtaatgtt tcagtccatc atccagcttt 10081ggctgctgaa atcatacagc tgtgaagact tgcctttgtt tctgttagac tgcttttcag 10141ttctgtattg agtatcttaa gtactgtaga aaagatgtca cttcttcctt taaggctgtt 10201ttgtaatata tataaggact ggaattgtgt ttttaaagaa aagcattcaa gtatgacaat 10261atactatctg tgttttcacc attcaaagtg ctgtttagta gttgaaactt aaactattta 10321atgtcattta ataaagtgac caaaatgtgt tgtgctcttt attgtatttt cacagctttg 10381aaaatctgtg cacatactgt ttcatagaaa atgtatagct tttgttgtcc tatataatgg 10441tggttctttt gcacatttag ttatttaata ttgagaggtc acgaagtttg gttattgaat 10501ctgttatata ctaaattctg taaagggaga tctctcatct caaaaagaat ttacatacca 10561ggaagtccat gtgtgtttgt gttagttttg gatgtctttg tgtaatccag ccccatttcc 10621tgtttcccaa cagctgtaac actcatttta agtcaagcag ggctaccaac ccacacttga 10681tagaaaagct gcttaccatt cagaagcttc cttattacct ggcctccaaa tgagctgaat 10741attttgtagc cttcccttag ctatgttcat tttccctcca ttatcataaa atcagatcga 10801tatttatgtg ccccaaacaa aactttaaga gcagttacat tctgtcccag tagcccttgt 10861ttcctttgag agtagcatgt tgtgaggcta tagagactta ttctaccagt aaaacaggtc 10921aatcctttta catgtttatt atactaaaaa ttatgttcag ggtatttact actttatttc 10981accagactca gtctcaagtg acttggctat ctccaaatca gatctaccct tagagaataa 11041acatttttct accgttattt tttttcaagt ctataatctg agccagtccc aaaggagtga 11101tcaagtttca gaaatgcttt catcttcaca acattttata tatactatta tatggggtga 11161ataaagtttt aaatccgaaa tataaaaaaa aaaaaaaaaa aaHomo sapiens alpha thalassemia/mental retardation syndrome X-linked (ATRX) isoform 2 (SEQ ID NO: 7)     1mtaepmsesk lntlvqklhd flahsseese etsspprlam nqntdkisgs gsnsdmmens    61keegtsssek skssgssrsk rkpsivtkyv esddekpldd etvnedasne nsenditmqs   121lpkedglhgi vsctacgqqv nhfqkdsiyr hpslqvlick ncfkyymsdd isrdsdgmde   181qcrwcaeggn liccdfchna fokkcilrnl grkelstimd ennqwycyic hpeplldlvt   241acnsvfenle qllqqnkkki kvdseksnkv yehtsrfspk ktssncngee kklddscsgs   301vtysysaliv pkemikkakk liettanmns syvkflkqat dnseissatk lrqlkafksv   361ladikkahla leedlnsefr amdavnkekn tkehkvidak fetkarkgek pcalekkdis   421kseaklsrkg vdsehmhqnv pteeqrtnks tggehkksdr keepqyepan tsedldmdiv   481svpssvpedi fenletamev qssvdhqgdg ssgteqeves ssvklnissk dnrggikskt   541takvtkelyv kltpvslsns pikgadcqev pqdkdgyksc glnpklekcg lggensdneh   601lvenevslll eesdlrrspr vkttplrrpt etnpvtsnsd eecnetvkek qklsvpvrkk   661dkrnssdsai dnpkpnklpk skqsetvdqn sdsdemlail kevsrmshss ssdtdineih   721tnhktlydlk tqagkddkgk rkrksstsgs dfdtkkgksa kssiiskkkr qtqsessnyd   781selekeiksm skigaarttk kripntkdfd ssedekhskk gmdnqghknl ktsgegssdd   841aerkqeretf ssaegtvdkd ttimelrdrl pkkqqasast dgvdklsgke qsftslevrk   901vaetkekskh lktktckkvg dglsdiaekf lkkdqsdets eddkkqskkg teekkkpsdf   961kkkvikmegq yesssdgtek lpereeichf pkgikqikng ttdgekkskk irdktskkkd  1021elsdyaekst gkgdscdsse dkkskngayg rekkrckllg kssrkrqdcs ssdtekysmk  1081edgcnssdkr lkrielrerr nlsskrntke iqsgssssda eessednkkk kqrtsskkka  1141vivkekkrns lrtstkrkqa ditsssssdi edddqnsige gssdeqkikp vtenlvlssh  1201tgfcgssgde alsksvpvtv ddddddndpe nriakkmlle eikanlssde dgssddepee  1261gkkrtgkqne enpgdeeakn qvnsesdsds eeskkpryrh rllrhkltvs dgesgeekkt  1321kpkehkevkg rnrrkvssed sedsdfqesg vseevsesed eqrprtrsak kaeleenqrs  1381ykqkkkrrri kvqedsssen ksnseeeeee keeeeeeeee eeeeeedend dskspgkgrk  1441kirkilkddk lrtetqnalk eeeerrkria ererereklr evieiedasp tkcpittklv  1501ldedeetkep lvqvhrnmvi klkphqvdgv qfmwdccces vkktkkspgs gcilahcmgl  1561gktlqvvsfl htvllcdkld fstalvvcpl ntalnwmnef ekwqeglkdd eklevselat  1621vkrpgersym lqrwqedggv miigyemyrn laqgrnvksr klkeifnkal vdpgpdfvvc  1681deghilknea sayskamnsi rsrrriiltg tplqnnliey hcmvnfiken llgsikefrn  1741rfinpiqngq cadstmvdvr vmkkrahily emlagcvqrk dytaltkflp pkheyvlavr  1801mtsiqcklyq yyldhltgvg nnseggrgka gaklfqdfqm lsriwthpwc lqldyisken  1861kgyfdedsmd efiasdsdet smslssddyt kkkkkgkkgk kdssssgsgs dndvevikvw  1921nsrsrgggeg nvdetgnnps vslkleeska tsssnpsspa pdwykdfvtd adaevlehsg  1981kmvllfeilr maeeigdkvl vfsqslisld liedflelas rektedkdkp liykgegkwl  2041rnidyyrldg sttaqsrkkw aeefndetnv rgrlfiistk agslginlva anrviifdas  2101wnpsydigsi frvyrfgqtk pvyvyrflaq gtmedkiydr qvtkqslsfr vvdqqqverh  2161ftmneltely tfepdllddp nsekkkkrdt pmlpkdtila ellqihkehi vgyhehdsll  2221dhkeeeelte eerkaawaey eaekkgltmr fniptgtnlp pvsfnsqtpy ipfnlgalsa  2281msnqqledli nqgrekvvea tnsvtavriq plediisavw kenmnlseaq vgalalsrqa  2341sqeldvkrre aiyndvltkq qmliscvgri lmnrrlqqqy nqqqqqqmty qqatlghlmm  2401pkppnlimnp snyqqidmrg myqpvaggmq ppplqrappp mrsknpgpsq gksmHomo sapiens alpha thalassemia/mental retardation syndrome X-linked (ATRX), transcript variant 2, mRNA (SEQ ID NO: 8)     1aattctcctg cctgagcctc ggcccaacaa aatggcggcg gcagcggtgt cgctttgttt    61ccgcggctcc tgcggcggtg gcagtggtag cggcctttga gctgtgggga ggttccagca   121gcagctacag tgacgactaa gactccagtg catttctatc gtaaccgggc gcgggggagc   181gcagatcggc gcccagcaat cacagaagcc gacaaggcgt tcaagcgaaa acatgaccgc   241tgagcccatg agtgaaagca agttgaatac attggtgcag aagcttcatg acttccttgc   301acactcatca gaagaatctg aagaaacaag ttctcctcca cgacttgcaa tgaatcaaaa   361cacagataaa atcagtggtt ctggaagtaa ctctgatatg atggaaaaca gcaaggaaga   421gggaactagc tcttcagaaa aatccaagtc ttcaggatcg tcacgatcaa agaggaaacc   481ttcaattgta acaaagtatg tagaatcaga tgatgaaaaa cctttggatg atgaaactgt   541aaatgaagat gcgtctaatg aaaattcaga aaatgatatt actatgcaga gcttgccaaa   601agaagatggg cttcatggga ttgtgagctg cactgcttgt ggacaacagg tcaatcattt   661tcaaaaagat tccatttata gacacccttc attgcaagtt cttatttgta agaattgctt   721taagtattac atgagtgatg atattagccg tgactcagat ggaatggatg aacaatgtag   781gtggtgtgcg gaaggtggaa acttgatttg ttgtgacttt tgccataatg ctttctgcaa   841gaaatgcatt ctacgcaacc ttggtcgaaa ggagttgtcc acaataatgg atgaaaacaa   901ccaatggtat tgctacattt gtcacccaga gcctttgttg gacttggtca ctgcatgtaa   961cagcgtattt gagaatttag aacagttgtt gcagcaaaat aagaagaaga taaaagttga  1021cagtgaaaag agtaataaag tatatgaaca tacatccaga ttttctccaa agaagactag  1081ttcaaattgt aatggagaag aaaagaaatt agatgattcc tgttctggct ctgtaaccta  1141ctcttattcc gcactaattg tgcccaaaga gatgattaag aaggcaaaaa aactgattga  1201gaccacagcc aacatgaact ccagttatgt taaattttta aagcaggcaa cagataattc  1261agaaatcagt tctgctacaa aattacgtca gcttaaggct tttaagtctg tgttggctga  1321tattaagaag gctcatcttg cattggaaga agacttaaat tccgagtttc gagcgatgga  1381tgctgtaaac aaagagaaaa ataccaaaga gcataaagtc atagatgcta agtttgaaac  1441aaaagcacga aaaggagaaa aaccttgtgc tttggaaaag aaggatattt caaagtcaga  1501agctaaactt tcaagaaaac aggtagatag tgagcacatg catcagaatg ttccaacaga  1561ggaacaaaga acaaataaaa gtaccggtgg tgaacataag aaatctgata gaaaagaaga  1621acctcaatat gaacctgcca acacttctga agatttagac atggatattg tgtctgttcc  1681ttcctcagtt ccagaagaca tttttgagaa tcttgagact gctatggaag ttcagagttc  1741agttgatcat caaggggatg gcagcagtgg aactgaacaa gaagtggaga gttcatctgt  1801aaaattaaat atttcttcaa aagacaacag aggaggtatt aaatcaaaaa ctacagctaa  1861agtaacaaaa gaattatatg ttaaactcac tcctgtttcc ctttctaatt ccccaattaa  1921aggtgctgat tgtcaggaag ttccacaaga taaagatggc tataaaagtt gtggtctgaa  1981ccccaagtta gagaaatgtg gacttggaca ggaaaacagt gataatgagc atttggttga  2041aaatgaagtt tcattacttt tagaggaatc tgatcttcga agatccccac gtgtaaagac  2101tacacccttg aggcgaccga cagaaactaa ccctgtaaca tctaattcag atgaagaatg  2161taatgaaaca gttaaggaga aacaaaaact atcagttcca gtgagaaaaa aggataagcg  2221taattcttct gacagtgcta tagataatcc taagcctaat aaattgccaa aatctaagca  2281atcagagact gtggatcaaa attcagattc tgatgaaatg ctagcaatcc tcaaagaggt  2341gagcaggatg agtcacagtt cttcttcaga tactgatatt aatgaaattc atacaaacca  2401taagactttg tatgatttaa agactcaggc ggggaaagat gataaaggaa aaaggaaacg  2461aaaaagttct acatctggct cagattttga tactaaaaag ggcaaatcag ctaagagctc  2521tataatttct aaaaagaaac gacaaaccca gtctgagtct tctaattatg actcagaatt  2581agaaaaagag ataaagagca tgagtaaaat tggtgctgcc agaaccacca aaaaaagaat  2641tccaaataca aaagattttg actcttctga agatgagaaa cacagcaaaa aaggaatgga  2701taatcaaggg cacaaaaatt tgaagacctc acaagaagga tcatctgatg atgctgaaag  2761aaaacaagag agagagactt tctcttcagc agaaggcaca gttgataaag acacgaccat  2821catggaatta agagatcgac ttcctaagaa gcagcaagca agtgcttcca ctgatggtgt  2881cgataagctt tctgggaaag agcagagttt tacttctttg gaagttagaa aagttgctga  2941aactaaagaa aagagcaagc atctcaaaac caaaacatgt aaaaaagtac aggatggctt  3001atctgatatt gcagagaaat tcctaaagaa agaccagagc gatgaaactt ctgaagatga  3061taaaaagcag agcaaaaagg gaactgaaga aaaaaagaaa ccttcagact ttaagaaaaa  3121agtaattaaa atggaacaac agtatgaatc ttcatctgat ggcactgaaa agttacctga  3181gcgagaagaa atttgtcatt ttcctaaggg cataaaacaa attaagaatg gaacaactga  3241tggagaaaag aaaagtaaaa aaataagaga taaaacttct aaaaagaagg atgaattatc  3301tgattatgct gagaagtcaa cagggaaagg agatagttgt gactcttcag aggataaaaa  3361gagtaagaat ggagcatatg gtagagagaa gaaaaggtgc aagttgcttg gaaagagttc  3421aaggaagaga caagattgtt catcatctga tactgagaaa tattccatga aagaagatgg  3481ttgtaactct tctgataaga gactgaaaag aatagaattg agggaaagaa gaaatttaag  3541ttcaaagaga aatactaagg aaatacaaag tggctcatca tcatctgatg ctgaggaaag  3601ttctgaagat aataaaaaga agaagcaaag aacttcatct aaaaagaagg cagtcattgt  3661caaggagaaa aagagaaact ccctaagaac aagcactaaa aggaagcaag ctgacattac  3721atcctcatct tcttctgata tagaagatga tgatcagaat tctataggtg agggaagcag  3781cgatgaacag aaaattaagc ctgtgactga aaatttagtg ctgtcttcac atactggatt  3841ttgccaatct tcaggagatg aagccttatc taaatcagtg cctgtcacag tggatgatga  3901tgatgacgac aatgatcctg agaatagaat tgccaagaag atgcttttag aagaaattaa  3961agccaatctt tcctctgatg aggatggatc ttcagatgat gagccagaag aagggaaaaa  4021aagaactgga aaacaaaatg aagaaaaccc aggagatgag gaagcaaaaa atcaagtcaa  4081ttctgaatca gattcagatt ctgaagaatc taagaagcca agatacagac ataggctttt  4141gcggcacaaa ttgactgtga gtgacggaga atctggagaa gaaaaaaaga caaagcctaa  4201agagcataaa gaagtcaaag gcagaaacag aagaaaggtg agcagtgaag attcagaaga  4261ttctgatttt caggaatcag gagttagtga agaagttagt gaatccgaag atgaacagcg  4321gcccagaaca aggtctgcaa agaaagcaga gttggaagaa aatcagcgga gctataaaca  4381gaaaaagaaa aggcgacgta ttaaggttca agaagattca tccagtgaaa acaagagtaa  4441ttctgaggaa gaagaggagg aaaaagaaga ggaggaggaa gaggaggagg aggaggaaga  4501ggaggaggaa gatgaaaatg atgattccaa gtctcctgga aaaggcagaa agaaaattcg  4561gaagattctt aaagatgata aactgagaac agaaacacaa aatgctctta aggaagagga  4621agagagacga aaacgtattg ctgagaggga gcgtgagcga gaaaaattga gagaggtgat  4681agaaattgaa gatgcttcac ccaccaagtg tccaataaca accaagttgg ttttagatga  4741agatgaagaa accaaagaac ctttagtgca ggttcataga aatatggtta tcaaattgaa  4801accccatcaa gtagatggtg ttcagtttat gtgggattgc tgctgtgagt ctgtgaaaaa  4861aacaaagaaa tctccaggtt caggatgcat tcttgcccac tgtatgggcc ttggtaagac  4921tttacaggtg gtaagttttc ttcatacagt tcttttgtgt gacaaactgg atttcagcac  4981ggcgttagtg gtttgtcctc ttaatactgc tttgaattgg atgaatgaat ttgagaagtg  5041gcaagaggga ttaaaagatg atgagaagct tgaggtttct gaattagcaa ctgtgaaacg  5101tcctcaggag agaagctaca tgctgcagag gtggcaagaa gatggtggtg ttatgatcat  5161aggctatgag atgtatagaa atcttgctca aggaaggaat gtgaagagtc ggaaacttaa  5221agaaatattt aacaaagctt tggttgatcc aggccctgat tttgttgttt gtgatgaagg  5281ccatattcta aaaaatgaag catctgctgt ttctaaagct atgaattcta tacgatcaag  5341gaggaggatt attttaacag gaacaccact tcaaaataac ctaattgagt atcattgtat  5401ggttaatttt atcaaggaaa atttacttgg atccattaag gagttcagga atagatttat  5461aaatccaatt caaaatggtc agtgtgcaga ttctaccatg gtagatgtca gagtgatgaa  5521aaaacgtgct cacattctct atgagatgtt agctggatgt gttcagagga aagattatac  5581agcattaaca aaattcttgc ctccaaaaca cgaatatgtg ttagctgtga gaatgacttc  5641tattcagtgc aagctctatc agtactactt agatcactta acaggtgtgg gcaataatag  5701tgaaggtgga agaggaaagg caggtgcaaa gcttttccaa gattttcaga tgttaagtag  5761aatatggact catccttggt gtttgcagct agactacatt agcaaagaaa ataagggtta  5821ttttgatgaa gacagtatgg atgaatttat agcctcagat tctgatgaaa cctccatgag  5881tttaagctcc gatgattata caaaaaagaa gaaaaaaggg aaaaagggga aaaaagatag  5941tagctcaagt ggaagtggca gtgacaatga tgttgaagtg attaaggtct ggaattcaag  6001atctcgggga ggtggtgaag gaaatgtgga tgaaacagga aacaatcctt ctgtttcttt  6061aaaactggaa gaaagtaaag ctacttcttc ttctaatcca agcagcccag ctccagactg  6121gtacaaagat tttgttacag atgctgatgc tgaggtttta gagcattctg ggaaaatggt  6181acttctcttt gaaattcttc gaatggcaga ggaaattggg gataaagtcc ttgttttcag  6241ccagtccctc atatctctgg acttgattga agattttctt gaattagcta gtagggagaa  6301gacagaagat aaagataaac cccttattta taaaggtgag gggaagtggc ttcgaaacat  6361tgactattac cgtttagatg gttccactac tgcacagtca aggaagaagt gggctgaaga  6421atttaatgat gaaactaatg tgagaggacg attatttatc atttctacta aagcaggatc  6481tctaggaatt aatctggtag ctgctaatcg agtaattata ttcgacgctt cttggaatcc  6541atcttatgac atccagagta tattcagagt ttatcgcttt ggacaaacta agcctgttta  6601tgtatatagg ttcttagctc agggaaccat ggaagataag atttatgatc ggcaagtaac  6661taagcagtca ctgtcttttc gagttgttga tcagcagcag gtggagcgtc attttactat  6721gaatgagctt actgaacttt atacttttga gccagactta ttagatgacc ctaattcaga  6781aaagaagaag aagagggata ctcccatgct gccaaaggat accatacttg cagagctcct  6841tcagatacat aaagaacaca ttgtaggata ccatgaacat gattctcttt tggaccacaa  6901agaagaagaa gagttgactg aagaagaaag aaaagcagct tgggctgagt atgaagcaga  6961gaagaaggga ctgaccatgc gtttcaacat accaactggg accaatttac cccctgtcag  7021tttcaactct caaactcctt atattccttt caatttggga gccctgtcag caatgagtaa  7081tcaacagctg gaggacctca ttaatcaagg aagagaaaaa gttgtagaag caacaaacag  7141tgtgacagca gtgaggattc aacctcttga ggatataatt tcagctgtat ggaaggagaa  7201catgaatctc tcagaggccc aagtacaggc gttagcatta agtagacaag ccagccagga  7261gcttgatgtt aaacgaagag aagcaatcta caatgatgta ttgacaaaac aacagatgtt  7321aatcagctgt gttcagcgaa tacttatgaa cagaaggctc cagcagcagt acaatcagca  7381gcaacagcaa caaatgactt atcaacaagc aacactgggt cacctcatga tgccaaagcc  7441cccaaatttg atcatgaatc cttctaacta ccagcagatt gatatgagag gaatgtatca  7501gccagtggct ggtggtatgc agccaccacc attacagcgt gcaccacccc caatgagaag  7561caaaaatcca ggaccttccc aagggaaatc aatgtgattt tgcactaaaa gcttaatgga  7621ttgttaaaat catagaaaga tcttttattt ttttaggaat caatgactta acagaactca  7681actgtataaa tagtttggtc cccttaaatg ccaatcttcc atattagttt tacttttttt  7741ttttttaaat agggcatacc atttcttcct gacatttgtc agtgatgttg cctagaatct  7801tcttacacac gctgagtaca gaagatattt caaattgttt tcagtgaaaa caagtccttc  7861cataatagta acaactccac agatttcctc tctaaatttt tatgcctgct tttagcaacc  7921ataaaattgt cataaaatta ataaatttag gaaagaataa agatttatat attcattctt  7981tacatataaa aacacacagc tgagttctta gagttgattc ctcaagttat gaaatacttt  8041tgtacttaat ccatttcttg attaaagtga ttgaaatggt tttaatgttc ttttgactga  8101agtctgaaac tgggctcctg ctttattgtc tctgtgactg aaagttagaa actgagggtt  8161atctttgaca cagaattgtg tgcaatattc ttaaatacta ctgctctaaa agttggagaa  8221gtcttgcagt tatcttagca ttgtataaac agccttaagt atagcctaag aagagaattc  8281ctttttcttc tttagtcctt ctgccatttt ttattttcag ttatatgtgc tgaaataatt  8341actggtaaaa tttcagggtt gtggattatc ttccacacat gaattttctc tctcctggca  8401cgaatataaa gcacatctct taactgcatg gtgccagtgc taatgcttca tcctgttgct  8461ggcagtggga tgtggactta gaaaatcaag ttctagcatt ttagtaggtt aacactgaag  8521ttgtggttgt taggttcaca ccctgtttta taaacaacat caaaatggca gaaccattgc  8581tgactttagg ttcacatgag gaatgtactt ttaacaattc ccagtactat cagtattgtg  8641aaataattcc tctgaaagat aagaatcact ggcttctatg cgcttctttt ctctcatcat  8701catgttcttt taccccagtt tccttacatt tttttaaatt gtttcagagt ttgttttttt  8761tttagtttag attgtgaggc aattattaaa tcaaaattaa ttcatccaat acccctttac  8821tagaagtttt actagaaaat gtattacatt ttattttttc ttaatccagt tctgcaaaaa  8881tgacctataa atttattcat gtacaatttt ggttacttga attgttaaag aaaacattgt  8941ttttgactat gggagtcaac tcaacatggc agaaccattt ttgagatgat gatacaacag  9001gtagtgaaac agcttaagaa ttccaaaaaa aaaaaaaaaa aaaaaaaaaa gaaaactggg  9061tttgggcttt gctttaggta tcactggatt agaatgagtt taacattagc taaaactgct  9121ttgagttgtt tggatgatta agagattgcc atttttatct tggaagaact agtggtaaaa  9181catccaagag cactaggatt gtgatacaga atttgtgagg tttggtggat ccacgcccct  9241ctcccccact ttcccatgat gaaatatcac taataaatcc tgtatattta gatattatgc  9301tagccatgta atcagattta tttaattggg tggggcaggt gtgtatttac tttagaaaaa  9361atgaaaaaga caagatttat gagaaatatt tgaaggcagt acactctggc caactgttac  9421cagttggtat ttctacaagt tcagaatatt ttaaacctga tttactagac ctgggaattt  9481tcaacatggt ctaattattt actcaaagac atagatgtga aaattttagg caaccttcta  9541aatctttttc accatggatg aaactataac ttaaagaata atacttagaa gggttaattg  9601gaaatcagag tttgaaataa aacttggacc actttgtata cactcttctc acttgacatt  9661ttagctatat aatatgtact ttgagtataa catcaagctt taacaaatat ttaaagacaa  9721aaaaatcacg tcagtaaaat actaaaaggc tcatttttat atttgtttta gatgttttaa  9781atagttgcaa tggattaaaa atgatgattt aaaatgttgc ttgtaataca gttttgcctg  9841ctaaattctc cacattttgt aacctgtttt atttctttgg gtgtaaagcg tttttgctta  9901gtattgtgat attgtatatg ttttgtccca gttgtatagt aatgtttcag tccatcatcc  9961agctttggct gctgaaatca tacagctgtg aagacttgcc tttgtttctg ttagactgct 10021tttcagttct gtattgagta tcttaagtac tgtagaaaag atgtcacttc ttcctttaag 10081gctgttttgt aatatatata aggactggaa ttgtgttttt aaagaaaagc attcaagtat 10141gacaatatac tatctgtgtt ttcaccattc aaagtgctgt ttagtagttg aaacttaaac 10201tatttaatgt catttaataa agtgaccaaa atgtgttgtg ctctttattg tattttcaca 10261gctttgaaaa tctgtgcaca tactgtttca tagaaaatgt atagcttttg ttgtcctata 10321taatggtggt tcttttgcac atttagttat ttaatattga gaggtcacga agtttggtta 10381ttgaatctgt tatatactaa attctgtaaa gggagatctc tcatctcaaa aagaatttac 10441ataccaggaa gtccatgtgt gtttgtgtta gttttggatg tctttgtgta atccagcccc 10501atttcctgtt tcccaacagc tgtaacactc attttaagtc aagcagggct accaacccac 10561acttgataga aaagctgctt accattcaga agcttcctta ttacctggcc tccaaatgag 10621ctgaatattt tgtagccttc ccttagctat gttcattttc cctccattat cataaaatca 10681gatcgatatt tatgtgcccc aaacaaaact ttaagagcag ttacattctg tcccagtagc 10741ccttgtttcc tttgagagta gcatgttgtg aggctataga gacttattct accagtaaaa 10801caggtcaatc cttttacatg tttattatac taaaaattat gttcagggta tttactactt 10861tatttcacca gactcagtct caagtgactt ggctatctcc aaatcagatc tacccttaga 10921gaataaacat ttttctaccg ttattttttt tcaagtctat aatctgagcc agtcccaaag 10981gagtgatcaa gtttcagaaa tgctttcatc ttcacaacat tttatatata ctattatatg 11041gggtgaataa agttttaaat ccgaaatata aaaaaaaaaa aaaaaaaa

A subject in need thereof may have reduced expression,haploinsufficiency, and/or loss of function of ARID1A. For example, asubject may comprise a mutation selected from the group consisting of anonsense mutation for the wild type residue cysteine (C) at amino acidposition 884 of SEQ ID NO: 11 (C884*), a substitution of lysine (K) forthe wild type residue glutamic acid (E) at amino acid position 966(E966K), a nonsense mutation for the wild type residue glutamine (Q) atamino acid position 1411 of SEQ ID NO: 11 (Q1411*), a frame shiftmutation at the wild type residue phenylalanine (F) at amino acidposition 1720 of SEQ ID NO: 11 (F1720fs), a frame shift mutation afterthe wild type residue glycine (G) at amino acid position 1847 of SEQ IDNO: 11 (G1847fs), a frame shift mutation at the wild type residuecysteine (C) at amino acid position 1874 of SEQ ID NO: 11 (C1874fs), asubstitution of glutamic acid (E) for the wild type residue asparticacid (D) at amino acid position 1957 (D1957E), a nonsense mutation forthe wild type residue glutamine (Q) at amino acid position 1430 of SEQID NO: 11 (Q1430*), a frame shift mutation at the wild type residuearginine (R) at amino acid position 1721 of SEQ ID NO: 11 (R1721fs), asubstitution of glutamic acid (E) for the wild type residue glycine (G)at amino acid position 1255 (G1255E), a frame shift mutation at the wildtype residue glycine (G) at amino acid position 284 of SEQ ID NO: 11(G284fs), a nonsense mutation for the wild type residue arginine (R) atamino acid position 1722 of SEQ ID NO: 11 (R1722*), a frame shiftmutation at the wild type residue methionine (M) at amino acid position274 of SEQ ID NO: 11 (M274fs), a frame shift mutation at the wild typeresidue glycine (G) at amino acid position 1847 of SEQ ID NO: 11(G1847fs), a frame shift mutation at the wild type residue P at aminoacid position 559 of SEQ ID NO: 11 (P559fs), a nonsense mutation for thewild type residue arginine (R) at amino acid position 1276 of SEQ ID NO:11 (R1276*), a frame shift mutation at the wild type residue glutamine(Q) at amino acid position 2176 of SEQ ID NO: 11 (Q2176fs), a frameshift mutation at the wild type residue histidine (H) at amino acidposition 203 of SEQ ID NO: 11 (H203fs), a frame shift mutation at thewild type residue alanine (A) at amino acid position 591 of SEQ ID NO:11 (A591fs), a nonsense mutation for the wild type residue glutamine (Q)at amino acid position 1322 of SEQ ID NO: 11 (Q1322*), a nonsensemutation for the wild type residue serine (S) at amino acid position2264 of SEQ ID NO: 11 (S2264*), a nonsense mutation for the wild typeresidue glutamine (Q) at amino acid position 586 of SEQ ID NO: 11(Q586*), a frame shift mutation at the wild type residue glutamine (Q)at amino acid position 548 of SEQ ID NO: 11 (Q548fs), and a frame shiftmutation at the wild type residue asparagine (N) at amino acid position756 of SEQ ID NO: 11 (N756fs). “*” used herein refers to a stop codon.“fs” used herein refers to a frame shift.

AT-rich interactive domain-containing protein 1A (ARID1A) isoform a[Homo sapiens] (SEQ ID NO: 9)    1maaqvapaaa sslgnppppp pselkkaeqq qreeaggeaa aaaaaergem kaaagqeseg   61pavgppqplg kelqdgaesn gggggggags gggpgaepdl knsngnagpr palnnnltep  121pggggggssd gvgapphsaa aalpppaygf gqpygrspsa vaaaaaavfh qqhggqqspg  181laalqsgggg glepyagpqq nshdhgfpnh qynsyypnrs aypppapaya lssprggtpg  241sgaaaaagsk pppsssasas sssssfaqqr fgamggggps aagggtpqpt atptlnqllt  301spssargyqg ypggdysggp qdggagkgpa dmasqcwgaa aaaaaaaaas ggaqqrshha  361pmspgssggg gqplartpqp sspmdqmgkm rpqpyggtnp ysqqqgppsg pqqghgypgq  421pygsqtpqry pmtmggraqs amgglsytqq ippygqqgps gygqqgqtpy ynggsphpqg  481qqppysqqpp sqtphaqpsy qqqpqsqppq lqssqppysq qpsqpphqqs papypsqqst  541tqqhpqsqpp ysqpqaqspy qqqqpqqpap stlsqqaayp qpqsqqsqqt aysqqrfppp  601qelsqdsfgs qassapsmts skggqedmnl slqsrpsslp dlsgsiddlp mgtegalspg  661vstsgisssq gegsnpagsp fsphtsphlp girgpspspv gspasvaqsr sgplspaavp  721gnqmpprpps gqsdsimhps mngssiaqdr gymqrnpqmp qysspqpgsa lsprqpsggq  781ihtgmgsyqq nsmgsygpqg gqygpqggyp rqpnynalpn anypsagmag ginpmgaggq  841mhgqpgippy gtlppgrmsh asmgnrpygp nmanmppqvg sgmcpppggm nrktqetava  901mhvaansiqn rppgypnmnq ggmmgtgppy gqginsmagm inpqgppysm ggtmannsag  961maaspemmgl gdvkltpatk mnnkadgtpk teskskksss stttnekitk lyelggeper 1021kmwvdrylaf teekamgmtn lpavgrkpld lyrlyvsvke iggltqvnkn kkwrelatnl 1081nvgtsssaas slkkqyiqcl yafeckierg edpppdifaa adskksqpki qppspagsgs 1141mqgpqtpqst sssmaeggdl kpptpastph sqipplpgms rsnsvgigda fndgsdstfq 1201krnsmtpnpg yqpsmntsdm mgrmsyepnk dpygsmrkap gsdpfmssgq gpnggmgdpy 1261sraagpglgn vamgprqhyp yggpydrvrt epgigpegnm stgapqpnlm psnpdsgmys 1321psryppqqqq qqqqrhdsyg nqfstqgtps gspfpsqqtt myqqqqqnyk rpmdgtygpp 1381akrhegemys vpystgqgqp qqqqlppaqp qpasqqqaaq pspqqdvynq ygnaypatat 1441aaterrpagg pqnqfpfqfg rdrvsappgt naqqnmppqm mggpigasae vaqqgtmwqg 1501rndmtynyan rqstgsapqg payhgvnrtd emlhtdqran hegswpshgt rqppygpsap 1561vppmtrppps nyqpppsmqn hipqvsspap lprpmenrts pskspflhsg mkmqkagppv 1621pashiapapv qppmirrdit fppgsveatq pvlkqrrrlt mkdigtpeaw rvmmslksgl 1681laestwaldt inillyddns imtfnlsqlp gllellveyf rrclieifgi lkeyevgdpg 1741qrtlldpgrf skvsspapme ggeeeeellg pkleeeeeee vvendeeiaf sgkdkpasen 1801seekliskfd klpvkivqkn dpfvvdcsdk lgrvqefdsg llhwrigggd ttehiqthfe 1861sktellpsrp hapcppaprk hvttaegtpg ttdqegpppd gppekritat mddmlstrss 1921tltedgakss eaikesskfp fgispaqshr nikiledeph skdetplctl ldwqdslakr 1981cvcvsntirs lsfvpgndfe mskhpgllli lgklillhhk hperkqaplt yekeeeqdqg 2041vscnkvewww dclemlrent lvtlanisgq ldlspypesi clpvldgllh wavcpsaeaq 2101dpfstlgpna vlspqrlvle tlsklsiqdn nvdlilatpp fsrleklyst mvrflsdrkn 2161pvcremavvl lanlaggdsl aaraiavqkg signllgfle dslaatqfqq sgasllhmqn 2221ppfeptsvdm mrraaralla lakvdenhse ftlyesrlld isysplmnsl vsqvicdvlf 2281ligqs Homo sapiens AT rich interactive domain 1A (SWI-like) (ARID1A),transcript variant 1, mRNA (SEQ ID NO: 10)    1cagaaagcgg agagtcacag cggggccagg ccctggggag cggagcctcc accgcccccc   61tcattcccag gcaagggctt ggggggaatg agccgggaga gccgggtccc gagcctacag  121agccgggagc agctgagccg ccggcgcctc ggccgccgcc gccgcctcct cctcctccgc  181cgccgccagc ccggagcctg agccggcggg gcggggggga gaggagcgag cgcagcgcag  241cagcggagcc ccgcgaggcc cgcccgggcg ggtggggagg gcagcccggg ggactgggcc  301ccggggcggg gtgggagggg gggagaagac gaagacaggg ccgggtctct ccgcggacga  361gacagcgggg atcatggccg cgcaggtcgc ccccgccgcc gccagcagcc tgggcaaccc  421gccgccgccg ccgccctcgg agctgaagaa agccgagcag cagcagcggg aggaggcggg  481gggcgaggcg gcggcggcgg cagcggccga gcgcggggaa atgaaggcag ccgccgggca  541ggaaagcgag ggccccgccg tggggccgcc gcagccgctg ggaaaggagc tgcaggacgg  601ggccgagagc aatgggggtg gcggcggcgg cggagccggc agcggcggcg ggcccggcgc  661ggagccggac ctgaagaact cgaacgggaa cgcgggccct aggcccgccc tgaacaataa  721cctcacggag ccgcccggcg gcggcggtgg cggcagcagc gatggggtgg gggcgcctcc  781tcactcagcc gcggccgcct tgccgccccc agcctacggc ttcgggcaac cctacggccg  841gagcccgtct gccgtcgccg ccgccgcggc cgccgtcttc caccaacaac atggcggaca  901acaaagccct ggcctggcag cgctgcagag cggcggcggc gggggcctgg agccctacgc  961ggggccccag cagaactctc acgaccacgg cttccccaac caccagtaca actcctacta 1021ccccaaccgc agcgcctacc ccccgcccgc cccggcctac gcgctgagct ccccgagagg 1081tggcactccg ggctccggcg cggcggcggc tgccggctcc aagccgcctc cctcctccag 1141cgcctccgcc tcctcgtcgt cttcgtcctt cgctcagcag cgcttcgggg ccatgggggg 1201aggcggcccc tccgcggccg gcgggggaac tccccagccc accgccaccc ccaccctcaa 1261ccaactgctc acgtcgccca gctcggcccg gggctaccag ggctaccccg ggggcgacta 1321cagtggcggg ccccaggacg ggggcgccgg caagggcccg gcggacatgg cctcgcagtg 1381ttggggggct gcggcggcgg cagctgcggc ggcggccgcc tcgggagggg cccaacaaag 1441gagccaccac gcgcccatga gccccgggag cagcggcggc ggggggcagc cgctcgcccg 1501gacccctcag ccatccagtc caatggatca gatgggcaag atgagacctc agccatatgg 1561cgggactaac ccatactcgc agcaacaggg acctccgtca ggaccgcagc aaggacatgg 1621gtacccaggg cagccatacg ggtcccagac cccgcagcgg tacccgatga ccatgcaggg 1681ccgggcgcag agtgccatgg gcggcctctc ttatacacag cagattcctc cttatggaca 1741acaaggcccc agcgggtatg gtcaacaggg ccagactcca tattacaacc agcaaagtcc 1801tcaccctcag cagcagcagc caccctactc ccagcaacca ccgtcccaga cccctcatgc 1861ccaaccttcg tatcagcagc agccacagtc tcaaccacca cagctccagt cctctcagcc 1921tccatactcc cagcagccat cccagcctcc acatcagcag tccccggctc catacccctc 1981ccagcagtcg acgacacagc agcaccccca gagccagccc ccctactcac agccacaggc 2041tcagtctcct taccagcagc agcaacctca gcagccagca ccctcgacgc tctcccagca 2101ggctgcgtat cctcagcccc agtctcagca gtcccagcaa actgcctatt cccagcagcg 2161cttccctcca ccgcaggagc tatctcaaga ttcatttggg tctcaggcat cctcagcccc 2221ctcaatgacc tccagtaagg gagggcaaga agatatgaac ctgagccttc agtcaagacc 2281ctccagcttg cctgatctat ctggttcaat agatgacctc cccatgggga cagaaggagc 2341tctgagtcct ggagtgagca catcagggat ttccagcagc caaggagagc agagtaatcc 2401agctcagtct cctttctctc ctcatacctc ccctcacctg cctggcatcc gaggcccttc 2461cccgtcccct gttggctctc ccgccagtgt tgctcagtct cgctcaggac cactctcgcc 2521tgctgcagtg ccaggcaacc agatgccacc tcggccaccc agtggccagt cggacagcat 2581catgcatcct tccatgaacc aatcaagcat tgcccaagat cgaggttata tgcagaggaa 2641cccccagatg ccccagtaca gttcccccca gcccggctca gccttatctc cgcgtcagcc 2701ttccggagga cagatacaca caggcatggg ctcctaccag cagaactcca tggggagcta 2761tggtccccag gggggtcagt atggcccaca aggtggctac cccaggcagc caaactataa 2821tgccttgccc aatgccaact accccagtgc aggcatggct ggaggcataa accccatggg 2881tgccggaggt caaatgcatg gacagcctgg catcccacct tatggcacac tccctccagg 2941gaggatgagt cacgcctcca tgggcaaccg gccttatggc cctaacatgg ccaatatgcc 3001acctcaggtt gggtcaggga tgtgtccccc accagggggc atgaaccgga aaacccaaga 3061aactgctgtc gccatgcatg ttgctgccaa ctctatccaa aacaggccgc caggctaccc 3121caatatgaat caagggggca tgatgggaac tggacctcct tatggacaag ggattaatag 3181tatggctggc atgatcaacc ctcagggacc cccatattcc atgggtggaa ccatggccaa 3241caattctgca gggatggcag ccagcccaga gatgatgggc cttggggatg taaagttaac 3301tccagccacc aaaatgaaca acaaggcaga tgggacaccc aagacagaat ccaaatccaa 3361gaaatccagt tcttctacta caaccaatga gaagatcacc aagttgtatg agctgggtgg 3421tgagcctgag aggaagatgt gggtggaccg ttatctggcc ttcactgagg agaaggccat 3481gggcatgaca aatctgcctg ctgtgggtag gaaacctctg gacctctatc gcctctatgt 3541gtctgtgaag gagattggtg gattgactca ggtcaacaag aacaaaaaat ggcgggaact 3601tgcaaccaac ctcaatgtgg gcacatcaag cagtgctgcc agctccttga aaaagcagta 3661tatccagtgt ctctatgcct ttgaatgcaa gattgaacgg ggagaagacc ctcccccaga 3721catctttgca gctgctgatt ccaagaagtc ccagcccaag atccagcctc cctctcctgc 3781gggatcagga tctatgcagg ggccccagac tccccagtca accagcagtt ccatggcaga 3841aggaggagac ttaaagccac caactccagc atccacacca cacagtcaga tccccccatt 3901gccaggcatg agcaggagca attcagttgg gatccaggat gcctttaatg atggaagtga 3961ctccacattc cagaagcgga attccatgac tccaaaccct gggtatcagc ccagtatgaa 4021tacctctgac atgatggggc gcatgtccta tgagccaaat aaggatcctt atggcagcat 4081gaggaaagct ccagggagtg atcccttcat gtcctcaggg cagggcccca acggcgggat 4141gggtgacccc tacagtcgtg ctgccggccc tgggctagga aatgtggcga tgggaccacg 4201acagcactat ccctatggag gtccttatga cagagtgagg acggagcctg gaatagggcc 4261tgagggaaac atgagcactg gggccccaca gccgaatctc atgccttcca acccagactc 4321ggggatgtat tctcctagcc gctacccccc gcagcagcag cagcagcagc agcaacgaca 4381tgattcctat ggcaatcagt tctccaccca aggcacccct tctggcagcc ccttccccag 4441ccagcagact acaatgtatc aacagcaaca gcagaattac aagcggccaa tggatggcac 4501atatggccct cctgccaagc ggcacgaagg ggagatgtac agcgtgccat acagcactgg 4561gcaggggcag cctcagcagc agcagttgcc cccagcccag ccccagcctg ccagccagca 4621acaagctgcc cagccttccc ctcagcaaga tgtatacaac cagtatggca atgcctatcc 4681tgccactgcc acagctgcta ctgagcgccg accagcaggc ggcccccaga accaatttcc 4741attccagttt ggccgagacc gtgtctctgc accccctggc accaatgccc agcaaaacat 4801gccaccacaa atgatgggcg gccccataca ggcatcagct gaggttgctc agcaaggcac 4861catgtggcag gggcgtaatg acatgaccta taattatgcc aacaggcaga gcacgggctc 4921tgccccccag ggccccgcct atcatggcgt gaaccgaaca gatgaaatgc tgcacacaga 4981tcagagggcc aaccacgaag gctcgtggcc ttcccatggc acacgccagc ccccatatgg 5041tccctctgcc cctgtgcccc ccatgacaag gccccctcca tctaactacc agcccccacc 5101aagcatgcag aatcacattc ctcaggtatc cagccctgct cccctgcccc ggccaatgga 5161gaaccgcacc tctcctagca agtctccatt cctgcactct gggatgaaaa tgcagaaggc 5221aggtccccca gtacctgcct cgcacatagc acctgcccct gtgcagcccc ccatgattcg 5281gcgggatatc accttcccac ctggctctgt tgaagccaca cagcctgtgt tgaagcagag 5341gaggcggctc acaatgaaag acattggaac cccggaggca tggcgggtaa tgatgtccct 5401caagtctggt ctcctggcag agagcacatg ggcattagat accatcaaca tcctgctgta 5461tgatgacaac agcatcatga ccttcaacct cagtcagctc ccagggttgc tagagctcct 5521tgtagaatat ttccgacgat gcctgattga gatctttggc attttaaagg agtatgaggt 5581gggtgaccca ggacagagaa cgctactgga tcctgggagg ttcagcaagg tgtctagtcc 5641agctcccatg gagggtgggg aagaagaaga agaacttcta ggtcctaaac tagaagagga 5701agaagaagag gaagtagttg aaaatgatga ggagatagcc ttttcaggca aggacaagcc 5761agcttcagag aatagtgagg agaagctgat cagtaagttt gacaagcttc cagtaaagat 5821cgtacagaag aatgatccat ttgtggtgga ctgctcagat aagcttgggc gtgtgcagga 5881gtttgacagt ggcctgctgc actggcggat tggtgggggg gacaccactg agcatatcca 5941gacccacttc gagagcaaga cagagctgct gccttcccgg cctcacgcac cctgcccacc 6001agcccctcgg aagcatgtga caacagcaga gggtacacca gggacaacag accaggaggg 6061gcccccacct gatggacctc cagaaaaacg gatcacagcc actatggatg acatgttgtc 6121tactcggtct agcaccttga ccgaggatgg agctaagagt tcagaggcca tcaaggagag 6181cagcaagttt ccatttggca ttagcccagc acagagccac cggaacatca agatcctaga 6241ggacgaaccc cacagtaagg atgagacccc actgtgtacc cttctggact ggcaggattc 6301tcttgccaag cgctgcgtct gtgtgtccaa taccattcga agcctgtcat ttgtgccagg 6361caatgacttt gagatgtcca aacacccagg gctgctgctc atcctgggca agctgatcct 6421gctgcaccac aagcacccag aacggaagca ggcaccacta acttatgaaa aggaggagga 6481acaggaccaa ggggtgagct gcaacaaagt ggagtggtgg tgggactgct tggagatgct 6541ccgggaaaac accttggtta cactcgccaa catctcgggg cagttggacc tatctccata 6601ccccgagagc atttgcctgc ctgtcctgga cggactccta cactgggcag tttgcccttc 6661agctgaagcc caggacccct tttccaccct gggccccaat gccgtccttt ccccgcagag 6721actggtcttg gaaaccctca gcaaactcag catccaggac aacaatgtgg acctgattct 6781ggccacaccc cccttcagcc gcctggagaa gttgtatagc actatggtgc gcttcctcag 6841tgaccgaaag aacccggtgt gccgggagat ggctgtggta ctgctggcca acctggctca 6901gggggacagc ctggcagctc gtgccattgc agtgcagaag ggcagtatcg gcaacctcct 6961gggcttccta gaggacagcc ttgccgccac acagttccag cagagccagg ccagcctcct 7021ccacatgcag aacccaccct ttgagccaac tagtgtggac atgatgcggc gggctgcccg 7081cgcgctgctt gccttggcca aggtggacga gaaccactca gagtttactc tgtacgaatc 7141acggctgttg gacatctcgg tatcaccgtt gatgaactca ttggtttcac aagtcatttg 7201tgatgtactg tttttgattg gccagtcatg acagccgtgg gacacctccc ccccccgtgt 7261gtgtgtgcgt gtgtggagaa cttagaaact gactgttgcc ctttatttat gcaaaaccac 7321ctcagaatcc agtttaccct gtgctgtcca gcttctccct tgggaaaaag tctctcctgt 7381ttctctctcc tccttccacc tcccctccct ccatcacctc acgcctttct gttccttgtc 7441ctcaccttac tcccctcagg accctacccc accctctttg aaaagacaaa gctctgccta 7501catagaagac tttttttatt ttaaccaaag ttactgttgt ttacagtgag tttggggaaa 7561aaaaataaaa taaaaatggc tttcccagtc cttgcatcaa cgggatgcca catttcataa 7621ctgtttttaa tggtaaaaaa aaaaaaaaaa aatacaaaaa aaaattctga aggacaaaaa 7681aggtgactgc tgaactgtgt gtggtttatt gttgtacatt cacaatcttg caggagccaa 7741gaagttcgca gttgtgaaca gaccctgttc actggagagg cctgtgcagt agagtgtaga 7801ccctttcatg tactgtactg tacacctgat actgtaaaca tactgtaata ataatgtctc 7861acatggaaac agaaaacgct gggtcagcag caagctgtag tttttaaaaa tgtttttagt 7921taaacgttga ggagaaaaaa aaaaaaggct tttcccccaa agtatcatgt gtgaacctac 7981aacaccctga cctctttctc tcctccttga ttgtatgaat aaccctgaga tcacctctta 8041gaactggttt taacctttag ctgcagcggc tacgctgcca cgtgtgtata tatatgacgt 8101tgtacattgc acataccctt ggatccccac agtttggtcc tcctcccagc taccccttta 8161tagtatgacg agttaacaag ttggtgacct gcacaaagcg agacacagct atttaatctc 8221ttgccagata tcgcccctct tggtgcgatg ctgtacaggt ctctgtaaaa agtccttgct 8281gtctcagcag ccaatcaact tatagtttat ttttttctgg gtttttgttt tgttttgttt 8341tctttctaat cgaggtgtga aaaagttcta ggttcagttg aagttctgat gaagaaacac 8401aattgagatt ttttcagtga taaaatctgc atatttgtat ttcaacaatg tagctaaaac 8461ttgatgtaaa ttcctccttt ttttcctttt ttggcttaat gaatatcatt tattcagtat 8521gaaatcttta tactatatgt tccacgtgtt aagaataaat gtacattaaa tcttggtaag 8581actttAT-rich interactive domain-containing protein 1A (ARID1A) isoform b(SEQ ID NO: 11)    1maaqvapaaa sslgnppppp pselkkaeqq qreeaggeaa aaaaaergem kaaagqeseg   61pavgppqplg kelqdgaesn gggggggags gggpgaepdl knsngnagpr palnnnltep  121pggggggssd gvgapphsaa aalpppaygf gqpygrspsa vaaaaaavfh qqhggqqspg  181laalqsgggg glepyagpqq nshdhgfpnh qynsyypnrs aypppapaya lssprggtpg  241sgaaaaagsk pppsssasas sssssfaqqr fgamggggps aagggtpqpt atptlnqllt  301spssargyqg ypggdysggp qdggagkgpa dmasqcwgaa aaaaaaaaas ggaqqrshha  361pmspgssggg gqplartpqp sspmdqmgkm rpqpyggtnp ysqqqgppsg pqqghgypgq  421pygsqtpqry pmtmggraqs amgglsytqq ippygqqgps gygqqgqtpy ynggsphpqg  481qqppysqqpp sqtphaqpsy qqqpqsqppq lqssqppysq qpsqpphqqs papypsqqst  541tqqhpqsqpp ysqpqaqspy qqqqpqqpap stlsqqaayp qpqsqqsqqt aysqqrfppp  601gelsqdsfgs qassapsmts skggqedmnl slqsrpsslp dlsgsiddlp mgtegalspg  661vstsgisssq gegsnpaqsp fsphtsphlp girgpspspv gspasvaqsr sgplspaavp  721gnqmpprpps gqsdsimhps mnqssiaqdr gymqrnpqmp qysspqpgsa lsprqpsggq  781ihtgmgsyqq nsmgsygpqg gqygpqggyp rqpnynalpn anypsagmag ginpmgaggq  841mhgqpgippy gtlppgrmsh asmgnrpygp nmanmppqvg sgmcpppggm nrktqetava  901mhvaansiqn rppgypnmnq ggmmgtgppy gqginsmagm inpqgppysm ggtmannsag  961maaspemmgl gdvkltpatk mnnkadgtpk teskskksss stttnekitk lyelggeper 1021kmwvdrylaf teekamgmtn lpavgrkpld lyrlyvsvke iggltqvnkn kkwrelatnl 1081nvgtsssaas slkkqyiqcl yafeckierg edpppdifaa adskksqpki qppspagsgs 1141mqgpqtpqst sssmaeggdl kpptpastph sqipplpgms rsnsvgiqda fndgsdstfq 1201krnsmtpnpg yqpsmntsdm mgrmsyepnk dpygsmrkap gsdpfmssgq gpnggmgdpy 1261sraagpglgn vamgprqhyp yggpydrvrt epgigpegnm stgapqpnlm psnpdsgmys 1321psryppqqqq qqqqrhdsyg nqfstqgtps gspfpsqqtt myqqqqqvss paplprpmen 1381rtspskspfl hsgmkmqkag ppvpashiap apvqppmirr ditfppgsve atqpvlkqrr 1441rltmkdigtp eawrvmmslk sgllaestwa ldtinillyd dnsimtfnls qlpgllellv 1501eyfrrcliei fgilkeyevg dpgqrtlldp grfskvsspa pmeggeeeee llgpkleeee 1561eeevvendee iafsgkdkpa senseeklis kfdklpvkiv qkndpfvvdc sdklgrvqef 1621dsgllhwrig ggdttehiqt hfesktellp srphapcppa prkhvttaeg tpgttdqegp 1681ppdgppekri tatmddmlst rsstltedga ksseaikess kfpfgispaq shrnikiled 1741ephskdetpl ctlldwgdsl akrcvcvsnt irslsfvpgn dfemskhpgl llilgklill 1801hhkhperkqa pltyekeeeq dqgvscnkve wwwdclemlr entivtlani sgqldlspyp 1861esiclpvldg llhwavcpsa eaqdpfstlg pnavlspqrl vletlsklsi qdnnvdlila 1921tppfsrlekl ystmvrflsd rknpvcrema vvllanlaqg dslaaraiav qkgsignllg 1981fledslaatq fqqsqasllh mqnppfepts vdmmrraara llalakvden hseftlyesr 2041lldisvsplm nslvsqvicd vlfligqsHomo sapiens AT rich interactive domain 1A (SWI-like) (ARID1A), transcript variant 2, mRNA (SEQ ID NO: 12)    1cagaaagcgg agagtcacag cggggccagg ccctggggag cggagcctcc accgcccccc   61tcattcccag gcaagggctt ggggggaatg agccgggaga gccgggtccc gagcctacag  121agccgggagc agctgagccg ccggcgcctc ggccgccgcc gccgcctcct cctcctccgc  181cgccgccagc ccggagcctg agccggcggg gcggggggga gaggagcgag cgcagcgcag  241cagcggagcc ccgcgaggcc cgcccgggcg ggtggggagg gcagcccggg ggactgggcc  301ccggggcggg gtgggagggg gggagaagac gaagacaggg ccgggtctct ccgcggacga  361gacagcgggg atcatggccg cgcaggtcgc ccccgccgcc gccagcagcc tgggcaaccc  421gccgccgccg ccgccctcgg agctgaagaa agccgagcag cagcagcggg aggaggcggg  481gggcgaggcg gcggcggcgg cagcggccga gcgcggggaa atgaaggcag ccgccgggca  541ggaaagcgag ggccccgccg tggggccgcc gcagccgctg ggaaaggagc tgcaggacgg  601ggccgagagc aatgggggtg gcggcggcgg cggagccggc agcggcggcg ggcccggcgc  661ggagccggac ctgaagaact cgaacgggaa cgcgggccct aggcccgccc tgaacaataa  721cctcacggag ccgcccggcg gcggcggtgg cggcagcagc gatggggtgg gggcgcctcc  781tcactcagcc gcggccgcct tgccgccccc agcctacggc ttcgggcaac cctacggccg  841gagcccgtct gccgtcgccg ccgccgcggc cgccgtcttc caccaacaac atggcggaca  901acaaagccct ggcctggcag cgctgcagag cggcggcggc gggggcctgg agccctacgc  961ggggccccag cagaactctc acgaccacgg cttccccaac caccagtaca actcctacta 1021ccccaaccgc agcgcctacc ccccgcccgc cccggcctac gcgctgagct ccccgagagg 1081tggcactccg ggctccggcg cggcggcggc tgccggctcc aagccgcctc cctcctccag 1141cgcctccgcc tcctcgtcgt cttcgtcctt cgctcagcag cgcttcgggg ccatgggggg 1201aggcggcccc tccgcggccg gcgggggaac tccccagccc accgccaccc ccaccctcaa 1261ccaactgctc acgtcgccca gctcggcccg gggctaccag ggctaccccg ggggcgacta 1321cagtggcggg ccccaggacg ggggcgccgg caagggcccg gcggacatgg cctcgcagtg 1381ttggggggct gcggcggcgg cagctgcggc ggcggccgcc tcgggagggg cccaacaaag 1441gagccaccac gcgcccatga gccccgggag cagcggcggc ggggggcagc cgctcgcccg 1501gacccctcag ccatccagtc caatggatca gatgggcaag atgagacctc agccatatgg 1561cgggactaac ccatactcgc agcaacaggg acctccgtca ggaccgcagc aaggacatgg 1621gtacccaggg cagccatacg ggtcccagac cccgcagcgg tacccgatga ccatgcaggg 1681ccgggcgcag agtgccatgg gcggcctctc ttatacacag cagattcctc cttatggaca 1741acaaggcccc agcgggtatg gtcaacaggg ccagactcca tattacaacc agcaaagtcc 1801tcaccctcag cagcagcagc caccctactc ccagcaacca ccgtcccaga cccctcatgc 1861ccaaccttcg tatcagcagc agccacagtc tcaaccacca cagctccagt cctctcagcc 1921tccatactcc cagcagccat cccagcctcc acatcagcag tccccggctc catacccctc 1981ccagcagtcg acgacacagc agcaccccca gagccagccc ccctactcac agccacaggc 2041tcagtctcct taccagcagc agcaacctca gcagccagca ccctcgacgc tctcccagca 2101ggctgcgtat cctcagcccc agtctcagca gtcccagcaa actgcctatt cccagcagcg 2161cttccctcca ccgcaggagc tatctcaaga ttcatttggg tctcaggcat cctcagcccc 2221ctcaatgacc tccagtaagg gagggcaaga agatatgaac ctgagccttc agtcaagacc 2281ctccagcttg cctgatctat ctggttcaat agatgacctc cccatgggga cagaaggagc 2341tctgagtcct ggagtgagca catcagggat ttccagcagc caaggagagc agagtaatcc 2401agctcagtct cctttctctc ctcatacctc ccctcacctg cctggcatcc gaggcccttc 2461cccgtcccct gttggctctc ccgccagtgt tgctcagtct cgctcaggac cactctcgcc 2521tgctgcagtg ccaggcaacc agatgccacc tcggccaccc agtggccagt cggacagcat 2581catgcatcct tccatgaacc aatcaagcat tgcccaagat cgaggttata tgcagaggaa 2641cccccagatg ccccagtaca gttcccccca gcccggctca gccttatctc cgcgtcagcc 2701ttccggagga cagatacaca caggcatggg ctcctaccag cagaactcca tggggagcta 2761tggtccccag gggggtcagt atggcccaca aggtggctac cccaggcagc caaactataa 2821tgccttgccc aatgccaact accccagtgc aggcatggct ggaggcataa accccatggg 2881tgccggaggt caaatgcatg gacagcctgg catcccacct tatggcacac tccctccagg 2941gaggatgagt cacgcctcca tgggcaaccg gccttatggc cctaacatgg ccaatatgcc 3001acctcaggtt gggtcaggga tgtgtccccc accagggggc atgaaccgga aaacccaaga 3061aactgctgtc gccatgcatg ttgctgccaa ctctatccaa aacaggccgc caggctaccc 3121caatatgaat caagggggca tgatgggaac tggacctcct tatggacaag ggattaatag 3181tatggctggc atgatcaacc ctcagggacc cccatattcc atgggtggaa ccatggccaa 3241caattctgca gggatggcag ccagcccaga gatgatgggc cttggggatg taaagttaac 3301tccagccacc aaaatgaaca acaaggcaga tgggacaccc aagacagaat ccaaatccaa 3361gaaatccagt tcttctacta caaccaatga gaagatcacc aagttgtatg agctgggtgg 3421tgagcctgag aggaagatgt gggtggaccg ttatctggcc ttcactgagg agaaggccat 3481gggcatgaca aatctgcctg ctgtgggtag gaaacctctg gacctctatc gcctctatgt 3541gtctgtgaag gagattggtg gattgactca ggtcaacaag aacaaaaaat ggcgggaact 3601tgcaaccaac ctcaatgtgg gcacatcaag cagtgctgcc agctccttga aaaagcagta 3661tatccagtgt ctctatgcct ttgaatgcaa gattgaacgg ggagaagacc ctcccccaga 3721catctttgca gctgctgatt ccaagaagtc ccagcccaag atccagcctc cctctcctgc 3781gggatcagga tctatgcagg ggccccagac tccccagtca accagcagtt ccatggcaga 3841aggaggagac ttaaagccac caactccagc atccacacca cacagtcaga tccccccatt 3901gccaggcatg agcaggagca attcagttgg gatccaggat gcctttaatg atggaagtga 3961ctccacattc cagaagcgga attccatgac tccaaaccct gggtatcagc ccagtatgaa 4021tacctctgac atgatggggc gcatgtccta tgagccaaat aaggatcctt atggcagcat 4081gaggaaagct ccagggagtg atcccttcat gtcctcaggg cagggcccca acggcgggat 4141gggtgacccc tacagtcgtg ctgccggccc tgggctagga aatgtggcga tgggaccacg 4201acagcactat ccctatggag gtccttatga cagagtgagg acggagcctg gaatagggcc 4261tgagggaaac atgagcactg gggccccaca gccgaatctc atgccttcca acccagactc 4321ggggatgtat tctcctagcc gctacccccc gcagcagcag cagcagcagc agcaacgaca 4381tgattcctat ggcaatcagt tctccaccca aggcacccct tctggcagcc ccttccccag 4441ccagcagact acaatgtatc aacagcaaca gcaggtatcc agccctgctc ccctgccccg 4501gccaatggag aaccgcacct ctcctagcaa gtctccattc ctgcactctg ggatgaaaat 4561gcagaaggca ggtcccccag tacctgcctc gcacatagca cctgcccctg tgcagccccc 4621catgattcgg cgggatatca ccttcccacc tggctctgtt gaagccacac agcctgtgtt 4681gaagcagagg aggcggctca caatgaaaga cattggaacc ccggaggcat ggcgggtaat 4741gatgtccctc aagtctggtc tcctggcaga gagcacatgg gcattagata ccatcaacat 4801cctgctgtat gatgacaaca gcatcatgac cttcaacctc agtcagctcc cagggttgct 4861agagctcctt gtagaatatt tccgacgatg cctgattgag atctttggca ttttaaagga 4921gtatgaggtg ggtgacccag gacagagaac gctactggat cctgggaggt tcagcaaggt 4981gtctagtcca gctcccatgg agggtgggga agaagaagaa gaacttctag gtcctaaact 5041agaagaggaa gaagaagagg aagtagttga aaatgatgag gagatagcct tttcaggcaa 5101ggacaagcca gcttcagaga atagtgagga gaagctgatc agtaagtttg acaagcttcc 5161agtaaagatc gtacagaaga atgatccatt tgtggtggac tgctcagata agcttgggcg 5221tgtgcaggag tttgacagtg gcctgctgca ctggcggatt ggtggggggg acaccactga 5281gcatatccag acccacttcg agagcaagac agagctgctg ccttcccggc ctcacgcacc 5341ctgcccacca gcccctcgga agcatgtgac aacagcagag ggtacaccag ggacaacaga 5401ccaggagggg cccccacctg atggacctcc agaaaaacgg atcacagcca ctatggatga 5461catgttgtct actcggtcta gcaccttgac cgaggatgga gctaagagtt cagaggccat 5521caaggagagc agcaagtttc catttggcat tagcccagca cagagccacc ggaacatcaa 5581gatcctagag gacgaacccc acagtaagga tgagacccca ctgtgtaccc ttctggactg 5641gcaggattct cttgccaagc gctgcgtctg tgtgtccaat accattcgaa gcctgtcatt 5701tgtgccaggc aatgactttg agatgtccaa acacccaggg ctgctgctca tcctgggcaa 5761gctgatcctg ctgcaccaca agcacccaga acggaagcag gcaccactaa cttatgaaaa 5821ggaggaggaa caggaccaag gggtgagctg caacaaagtg gagtggtggt gggactgctt 5881ggagatgctc cgggaaaaca ccttggttac actcgccaac atctcggggc agttggacct 5941atctccatac cccgagagca tttgcctgcc tgtcctggac ggactcctac actgggcagt 6001ttgcccttca gctgaagccc aggacccctt ttccaccctg ggccccaatg ccgtcctttc 6061cccgcagaga ctggtcttgg aaaccctcag caaactcagc atccaggaca acaatgtgga 6121cctgattctg gccacacccc ccttcagccg cctggagaag ttgtatagca ctatggtgcg 6181cttcctcagt gaccgaaaga acccggtgtg ccgggagatg gctgtggtac tgctggccaa 6241cctggctcag ggggacagcc tggcagctcg tgccattgca gtgcagaagg gcagtatcgg 6301caacctcctg ggcttcctag aggacagcct tgccgccaca cagttccagc agagccaggc 6361cagcctcctc cacatgcaga acccaccctt tgagccaact agtgtggaca tgatgcggcg 6421ggctgcccgc gcgctgcttg ccttggccaa ggtggacgag aaccactcag agtttactct 6481gtacgaatca cggctgttgg acatctcggt atcaccgttg atgaactcat tggtttcaca 6541agtcatttgt gatgtactgt ttttgattgg ccagtcatga cagccgtggg acacctcccc 6601cccccgtgtg tgtgtgcgtg tgtggagaac ttagaaactg actgttgccc tttatttatg 6661caaaaccacc tcagaatcca gtttaccctg tgctgtccag cttctccctt gggaaaaagt 6721ctctcctgtt tctctctcct ccttccacct cccctccctc catcacctca cgcctttctg 6781ttccttgtcc tcaccttact cccctcagga ccctacccca ccctctttga aaagacaaag 6841ctctgcctac atagaagact ttttttattt taaccaaagt tactgttgtt tacagtgagt 6901ttggggaaaa aaaataaaat aaaaatggct ttcccagtcc ttgcatcaac gggatgccac 6961atttcataac tgtttttaat ggtaaaaaaa aaaaaaaaaa atacaaaaaa aaattctgaa 7021ggacaaaaaa ggtgactgct gaactgtgtg tggtttattg ttgtacattc acaatcttgc 7081aggagccaag aagttcgcag ttgtgaacag accctgttca ctggagaggc ctgtgcagta 7141gagtgtagac cctttcatgt actgtactgt acacctgata ctgtaaacat actgtaataa 7201taatgtctca catggaaaca gaaaacgctg ggtcagcagc aagctgtagt ttttaaaaat 7261gtttttagtt aaacgttgag gagaaaaaaa aaaaaggctt ttcccccaaa gtatcatgtg 7321tgaacctaca acaccctgac ctctttctct cctccttgat tgtatgaata accctgagat 7381cacctcttag aactggtttt aacctttagc tgcagcggct acgctgccac gtgtgtatat 7441atatgacgtt gtacattgca catacccttg gatccccaca gtttggtcct cctcccagct 7501acccctttat agtatgacga gttaacaagt tggtgacctg cacaaagcga gacacagcta 7561tttaatctct tgccagatat cgcccctctt ggtgcgatgc tgtacaggtc tctgtaaaaa 7621gtccttgctg tctcagcagc caatcaactt atagtttatt tttttctggg tttttgtttt 7681gttttgtttt ctttctaatc gaggtgtgaa aaagttctag gttcagttga agttctgatg 7741aagaaacaca attgagattt tttcagtgat aaaatctgca tatttgtatt tcaacaatgt 7801agctaaaact tgatgtaaat tcctcctttt tttccttttt tggcttaatg aatatcattt 7861attcagtatg aaatctttat actatatgtt ccacgtgtta agaataaatg tacattaaat 7921cttggtaaga cttt

The present invention also provides methods of inducing neuronaldifferentiation by contacting a cell with a compound (i.e., an EZH2inhibitor) of the invention. Preferably, the compound is in an amountsufficient to increase expression of at least one gene selected from thegroup consisting of CD133 (also called PROM1), DOCK4, PTPRK, PROM2,LHX1, LHX6, LHX9, PAX6, PAX7, VEFGA, FZD3B, FYN, HIF1A, HTRA2, EVX1,CCDC64, and GFAP.

The term “inducing neuronal differentiation” used herein refers tocausing a cell to develop into a cell of the neuronal lineage as aresult of a direct or intentional effect on the cell.

The present invention also provides methods of inducing cell cycleinhibition by contacting a cell with a compound of the invention.Preferably, the compound is in an amount sufficient to increaseexpression of at least one gene selected from the group consisting ofCKDN1A, CDKN2A, MEN1, CHEK1, IRF6, ALOX15B, CYP27B1, DBC1, NME6, GMNN,HEXIM1, LATS1, MYC, HRAS, TGFB1, IFNG, WNT1, TP53, THBS1, INHBA, IL8,IRF1, TPR, BMP2, BMP4, ETS1, HPGD, BMP7, GATA3, NR2F2, APC, PTPN3, CALR,IL12A, IL12B, PML, CDKN2B, CDKN2C, CDKN1B, SOX2, TAF6, DNA2, PLK1,TERF1, GAS1, CDKN2D, MLF1, PTEN, TGFB2, SMAD3, FOXO4, CDK6, TFAP4,MAP2K1, NOTCH2, FOXC1, DLG1, MAD2L1, ATM, NAE1, DGKZ, FHL1, SCRIB, BTG3,PTPRK, RPS6KA2, STK11, CDKN3, TBRG1, CDC73, THAP5, CRLF3, DCUN1D3,MYOCD, PAF1, LILRB1, UHMK1, PNPT1, USP47, HEXIM2, CDK5RAP1, NKX3-1,TIPIN, PCBP4, USP44, RBM38, CDT1, RGCC, RNF167, CLSPN, CHMP1A, WDR6,TCF7L2, LATS2, RASSF1, MLTK, MAD2L2, FBXO5, ING4, and TRIM35.

The term “inducing cell cycle inhibition” used herein refers to causingan accumulation or an arrest at any phase during cell division and/orduplication.

The present invention also provides methods of inducing tumorsuppression by contacting a cell with a compound of the invention.Preferably, the compound is in an amount sufficient to increaseexpression of BIN1 or any tumor suppressors.

The term “inducing tumor suppression” may include, but is not limitedto, a reduction in size of a tumor, a reduction in tumor volume, adecrease in number of tumors, a decrease in number of metastatic lesionsin other tissues or organs distant from the primary tumor site, anincrease in average survival time of a population of treated subjects incomparison to a population receiving carrier alone, an increase inaverage survival time of a population of treated subjects in comparisonto a population of untreated subjects, an increase in average survivaltime of a population of treated subjects in comparison to a populationreceiving monotherapy with a drug that is not a compound of the presentinvention, a decrease in the mortality rate of a population of treatedsubjects in comparison to a population receiving carrier alone, adecrease in tumor growth rate, or a decrease in tumor regrowth rate.

The present invention also provides methods of inhibiting hedgehogsignaling by contacting a cell with a compound of the invention.Preferably, the compound is in an amount sufficient to reduce expressionof at least one gene selected from the group consisting of GLI1, PTCH1,SUFU, KIF7, GLI2, BMP4, MAP3K10, SHH, TCTN3, DYRK2, PTCHD1, and SMO.

The phrase “inhibiting hedgehog signaling” means the hedgehog signalingstrength (intensity) with a compound treatment is reduced by at least5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%,75%, 80%, 85%, 90%, 95%, 100%, 200%, 300%, 400%, 500%, 1000%, 1500%, ormore compared to the hedgehog signaling strength (intensity) without anycompound treatment.

The present invention also provides methods of inducing a geneexpression by contacting a cell with a compound of the invention.Preferably, the compound is in an amount sufficient to induce neuronaldifferentiation, cell cycle inhibition and/or tumor suppression. Suchgene is selected from the group consisting of CD133 (also called PROM1),DOCK4, PTPRK, PROM2, LHX1, LHX6, LHX9, PAX6, PAX7, VEFGA, FZD3B, FYN,HIF1A, HTRA2, EVX1, CCDC64, GFAP, CKDN1A, CDKN2A, MEN1, CHEK1, IRF6,ALOX15B, CYP27B1, DBC1, NME6, GMNN, HEXIM1, LATS1, MYC, HRAS, TGFB1,IFNG, WNT1, TP53, THBS1, INHBA, IL8, IRF1, TPR, BMP2, BMP4, ETS1, HPGD,BMP7, GATA3, NR2F2, APC, PTPN3, CALR, IL12A, IL12B, PML, CDKN2B, CDKN2C,CDKN1B, SOX2, TAF6, DNA2, PLK1, TERF1, GAS1, CDKN2D, MLF1, PTEN, TGFB2,SMAD3, FOXO4, CDK6, TFAP4, MAP2K1, NOTCH2, FOXC1, DLG1, MAD2L1, ATM,NAE1, DGKZ, FHL1, SCRIB, BTG3, PTPRK, RPS6KA2, STK11, CDKN3, TBRG1,CDC73, THAP5, CRLF3, DCUN1D3, MYOCD, PAF1, LILRB1, UHMK1, PNPT1, USP47,HEXIM2, CDK5RAP1, NKX3-1, TIPIN, PCBP4, USP44, RBM38, CDT1, RGCC,RNF167, CLSPN, CHMP1A, WDR6, TCF7L2, LATS2, RASSF1, MLTK, MAD2L2, FBXO5,ING4, TRIM35, BIN1 and any tumor suppressors.

The phrase “inducing a gene expression” means the expression level of aparticular gene of interest is increased by at least 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 100%, 200%, 300%, 400%, 500%, 1000%, 1500%, or more compared to theexpression level of this gene without any compound treatment.

The present invention also provides methods of inhibiting a geneexpression comprising contacting a cell with a compound of theinvention. Preferably, the compound is in an amount sufficient toinhibit hedgehog signaling. Such gene is GLI1, PTCH1, SUFU, KIF7, GLI2,BMP4, MAP3K10, SHH, TCTN3, DYRK2, PTCHD1, or SMO.

The phrase “inhibiting a gene expression” means the expression level ofa particular gene of interest is reduced by at least 5%, 10%, 15%, 20%,25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, 100%, 200%, 300%, 400%, 500%, 1000%, 1500%, or more compared to theexpression level of this gene without any compound treatment.

Neuronal differentiation, cell cycle inhibition, tumor suppression andhedgehog signaling inhibition can be determined by any methods known inthe art.

As used herein, a cell refers to any cell that can be obtained and usedby a method described herein. For example, a cell may be obtained from acell culture. Alternatively, a cell may be isolated from a subject. Acell may also refer to a cell of a subject.

A cell may comprise loss of function of SNF5, ARID1A, ATRX, and/or acomponent of the SWI/SNF complex. Preferably, a cell may comprise adeletion of SNF5.

A cell may be a cancer cell, where the cancer is selected from the groupconsisting of medulloblastoma, oligodendroglioma, ovarian clear celladenocarcinoma, ovarian endomethrioid adenocarcinoma, ovarian serousadenocarcinoma, pancreatic ductal adenocarcinoma, pancreatic endocrinetumor, malignant rhabdoid tumor, astrocytoma, atypical teratoid rhabdoidtumor, choroid plexus carcinoma, choroid plexus papilloma, ependymoma,glioblastoma, meningioma, neuroglial tumor, oligoastrocytoma,oligodendroglioma, pineoblastoma, carcinosarcoma, chordoma, extragonadalgerm cell tumor, extrarenal rhabdoid tumor, schwannoma, skin squamouscell carcinoma, chondrosarcoma, clear cell sarcoma of soft tissue, ewingsarcoma, gastrointestinal stromal tumor, osteosarcoma, rhabdomyosarcoma,epithelioid sarcoma, renal medullo carcinoma, diffuse large B-celllymphoma, follicular lymphoma and not otherwise specified (NOS) sarcoma.More preferably a cell is a cancer cell of medulloblastoma, malignantrhabdoid tumor, or atypical teratoid rhabdoid tumor.

A cancer that is to be treated can be staged according to the AmericanJoint Committee on Cancer (AJCC) TNM classification system, where thetumor (T) has been assigned a stage of TX, T1, T1mic, T1a, T1b, T1c, T2,T3, T4, T4a, T4b, T4c, or T4d; and where the regional lymph nodes (N)have been assigned a stage of NX, N0, N1, N2, N2a, N2b, N3, N3a, N3b, orN3c; and where distant metastasis (M) can be assigned a stage of MX, M0,or M1. A cancer that is to be treated can be staged according to anAmerican Joint Committee on Cancer (AJCC) classification as Stage I,Stage IIA, Stage IIB, Stage IIIA, Stage IIIB, Stage IIIC, or Stage IV. Acancer that is to be treated can be assigned a grade according to anAJCC classification as Grade GX (e.g., grade cannot be assessed), Grade1, Grade 2, Grade 3 or Grade 4. A cancer that is to be treated can bestaged according to an AJCC pathologic classification (pN) of pNX, pN0,PN0 (I−), PN0 (I+), PN0 (mol−), PN0 (mol+), PN1, PN1(mi), PN1a, PN1b,PN1c, pN2, pN2a, pN2b, pN3, pN3a, pN3b, or pN3c.

A cancer that is to be treated can be evaluated by DNA cytometry, flowcytometry, or image cytometry. A cancer that is to be treated can betyped as having 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, or 90% of cellsin the synthesis stage of cell division (e.g., in S phase of celldivision). A cancer that is to be treated can be typed as having a lowS-phase fraction or a high S-phase fraction.

As used herein, a “normal cell” is a cell that cannot be classified aspart of a “cell proliferative disorder”. A normal cell lacks unregulatedor abnormal growth, or both, that can lead to the development of anunwanted condition or disease. Preferably, a normal cell possessesnormally functioning cell cycle checkpoint control mechanisms.

As used herein, “contacting a cell” refers to a condition in which acompound or other composition of matter is in direct contact with acell, or is close enough to induce a desired biological effect in acell.

As used herein, “monotherapy” refers to the administration of a singleactive or therapeutic compound to a subject in need thereof. Preferably,monotherapy will involve administration of a therapeutically effectiveamount of an active compound. For example, cancer monotherapy with oneof the compound of the present invention, or a pharmaceuticallyacceptable salt, polymorph, solvate, analog or derivative thereof, to asubject in need of treatment of cancer. Monotherapy may be contrastedwith combination therapy, in which a combination of multiple activecompounds is administered, preferably with each component of thecombination present in a therapeutically effective amount. In oneaspect, monotherapy with a compound of the present invention, or apharmaceutically acceptable salt, polymorph or solvate thereof, is moreeffective than combination therapy in inducing a desired biologicaleffect.

As used herein, “treating” or “treat” describes the management and careof a patient for the purpose of combating a disease, condition, ordisorder and includes the administration of a compound of the presentinvention, or a pharmaceutically acceptable salt, polymorph or solvatethereof, to alleviate one or more symptoms or complications of adisease, condition or disorder, or to eliminate the disease, conditionor disorder. The term “treat” can also include treatment of a cell invitro or an animal model.

A compound of the present invention, or a pharmaceutically acceptablesalt, polymorph or solvate thereof, can also be used to prevent adisease, condition or disorder, or used to identify suitable candidatesfor such purposes. As used herein, “preventing” or “prevent” describesreducing or eliminating the onset of the symptoms or complications ofthe disease, condition or disorder.

As used herein, the term “alleviate” is meant to describe a process bywhich the severity of a sign or symptom of a disorder is decreased.Importantly, a sign or symptom can be alleviated without beingeliminated. In a preferred embodiment, the administration ofpharmaceutical compositions of the invention leads to the elimination ofa sign or symptom, however, elimination is not required. Effectivedosages are expected to decrease the severity of a sign or symptom. Forinstance, a sign or symptom of a disorder such as cancer, which canoccur in multiple locations, is alleviated if the severity of the canceris decreased within at least one of multiple locations.

As used herein, the term “severity” is meant to describe the potentialof cancer to transform from a precancerous, or benign, state into amalignant state. Alternatively, or in addition, severity is meant todescribe a cancer stage, for example, according to the TNM system(accepted by the International Union Against Cancer (UICC) and theAmerican Joint Committee on Cancer (AJCC)) or by other art-recognizedmethods. Cancer stage refers to the extent or severity of the cancer,based on factors such as the location of the primary tumor, tumor size,number of tumors, and lymph node involvement (spread of cancer intolymph nodes). Alternatively, or in addition, severity is meant todescribe the tumor grade by art-recognized methods (see, National CancerInstitute, www.cancer.gov). Tumor grade is a system used to classifycancer cells in terms of how abnormal they look under a microscope andhow quickly the tumor is likely to grow and spread. Many factors areconsidered when determining tumor grade, including the structure andgrowth pattern of the cells. The specific factors used to determinetumor grade vary with each type of cancer. Severity also describes ahistologic grade, also called differentiation, which refers to how muchthe tumor cells resemble normal cells of the same tissue type (see,National Cancer Institute, www.cancer.gov). Furthermore, severitydescribes a nuclear grade, which refers to the size and shape of thenucleus in tumor cells and the percentage of tumor cells that aredividing (see, National Cancer Institute, www.cancer.gov).

In another aspect of the invention, severity describes the degree towhich a tumor has secreted growth factors, degraded the extracellularmatrix, become vascularized, lost adhesion to juxtaposed tissues, ormetastasized. Moreover, severity describes the number of locations towhich a primary tumor has metastasized. Finally, severity includes thedifficulty of treating tumors of varying types and locations. Forexample, inoperable tumors, those cancers which have greater access tomultiple body systems (hematological and immunological tumors), andthose which are the most resistant to traditional treatments areconsidered most severe. In these situations, prolonging the lifeexpectancy of the subject and/or reducing pain, decreasing theproportion of cancerous cells or restricting cells to one system, andimproving cancer stage/tumor grade/histological grade/nuclear grade areconsidered alleviating a sign or symptom of the cancer.

As used herein the term “symptom” is defined as an indication ofdisease, illness, injury, or that something is not right in the body.Symptoms are felt or noticed by the individual experiencing the symptom,but may not easily be noticed by others. Others are defined asnon-health-care professionals.

As used herein the term “sign” is also defined as an indication thatsomething is not right in the body. But signs are defined as things thatcan be seen by a doctor, nurse, or other health care professional.

Cancer is a group of diseases that may cause almost any sign or symptom.The signs and symptoms will depend on where the cancer is, the size ofthe cancer, and how much it affects the nearby organs or structures. Ifa cancer spreads (metastasizes), then symptoms may appear in differentparts of the body.

Treating cancer can result in a reduction in size of a tumor. Areduction in size of a tumor may also be referred to as “tumorregression”. Preferably, after treatment, tumor size is reduced by 5% orgreater relative to its size prior to treatment; more preferably, tumorsize is reduced by 10% or greater; more preferably, reduced by 20% orgreater; more preferably, reduced by 30% or greater; more preferably,reduced by 40% or greater; even more preferably, reduced by 50% orgreater; and most preferably, reduced by greater than 75% or greater.Size of a tumor may be measured by any reproducible means ofmeasurement. The size of a tumor may be measured as a diameter of thetumor.

Treating cancer can result in a reduction in tumor volume. Preferably,after treatment, tumor volume is reduced by 5% or greater relative toits size prior to treatment; more preferably, tumor volume is reduced by10% or greater; more preferably, reduced by 20% or greater; morepreferably, reduced by 30% or greater; more preferably, reduced by 40%or greater; even more preferably, reduced by 50% or greater; and mostpreferably, reduced by greater than 75% or greater. Tumor volume may bemeasured by any reproducible means of measurement.

Treating cancer results in a decrease in number of tumors. Preferably,after treatment, tumor number is reduced by 5% or greater relative tonumber prior to treatment; more preferably, tumor number is reduced by10% or greater; more preferably, reduced by 20% or greater; morepreferably, reduced by 30% or greater; more preferably, reduced by 40%or greater; even more preferably, reduced by 50% or greater; and mostpreferably, reduced by greater than 75%. Number of tumors may bemeasured by any reproducible means of measurement. The number of tumorsmay be measured by counting tumors visible to the naked eye or at aspecified magnification. Preferably, the specified magnification is 2×,3×, 4×, 5×, 10×, or 50×.

Treating cancer can result in a decrease in number of metastatic lesionsin other tissues or organs distant from the primary tumor site.Preferably, after treatment, the number of metastatic lesions is reducedby 5% or greater relative to number prior to treatment; more preferably,the number of metastatic lesions is reduced by 10% or greater; morepreferably, reduced by 20% or greater; more preferably, reduced by 30%or greater; more preferably, reduced by 40% or greater; even morepreferably, reduced by 50% or greater; and most preferably, reduced bygreater than 75%. The number of metastatic lesions may be measured byany reproducible means of measurement. The number of metastatic lesionsmay be measured by counting metastatic lesions visible to the naked eyeor at a specified magnification. Preferably, the specified magnificationis 2×, 3×, 4×, 5×, 10×, or 50×.

Treating cancer can result in an increase in average survival time of apopulation of treated subjects in comparison to a population receivingcarrier alone. Preferably, the average survival time is increased bymore than 30 days; more preferably, by more than 60 days; morepreferably, by more than 90 days; and most preferably, by more than 120days. An increase in average survival time of a population may bemeasured by any reproducible means. An increase in average survival timeof a population may be measured, for example, by calculating for apopulation the average length of survival following initiation oftreatment with an active compound. An increase in average survival timeof a population may also be measured, for example, by calculating for apopulation the average length of survival following completion of afirst round of treatment with an active compound.

Treating cancer can result in an increase in average survival time of apopulation of treated subjects in comparison to a population ofuntreated subjects. Preferably, the average survival time is increasedby more than 30 days; more preferably, by more than 60 days; morepreferably, by more than 90 days; and most preferably, by more than 120days. An increase in average survival time of a population may bemeasured by any reproducible means. An increase in average survival timeof a population may be measured, for example, by calculating for apopulation the average length of survival following initiation oftreatment with an active compound. An increase in average survival timeof a population may also be measured, for example, by calculating for apopulation the average length of survival following completion of afirst round of treatment with an active compound.

Treating cancer can result in increase in average survival time of apopulation of treated subjects in comparison to a population receivingmonotherapy with a drug that is not a compound of the present invention,or a pharmaceutically acceptable salt, polymorph, solvate, analog orderivative thereof. Preferably, the average survival time is increasedby more than 30 days; more preferably, by more than 60 days; morepreferably, by more than 90 days; and most preferably, by more than 120days. An increase in average survival time of a population may bemeasured by any reproducible means. An increase in average survival timeof a population may be measured, for example, by calculating for apopulation the average length of survival following initiation oftreatment with an active compound. An increase in average survival timeof a population may also be measured, for example, by calculating for apopulation the average length of survival following completion of afirst round of treatment with an active compound.

Treating cancer can result in a decrease in the mortality rate of apopulation of treated subjects in comparison to a population receivingcarrier alone. Treating cancer can result in a decrease in the mortalityrate of a population of treated subjects in comparison to an untreatedpopulation. Treating cancer can result in a decrease in the mortalityrate of a population of treated subjects in comparison to a populationreceiving monotherapy with a drug that is not a compound of the presentinvention, or a pharmaceutically acceptable salt, polymorph, solvate,analog or derivative thereof. Preferably, the mortality rate isdecreased by more than 2%; more preferably, by more than 5%; morepreferably, by more than 10%; and most preferably, by more than 25%. Adecrease in the mortality rate of a population of treated subjects maybe measured by any reproducible means. A decrease in the mortality rateof a population may be measured, for example, by calculating for apopulation the average number of disease-related deaths per unit timefollowing initiation of treatment with an active compound. A decrease inthe mortality rate of a population may also be measured, for example, bycalculating for a population the average number of disease-relateddeaths per unit time following completion of a first round of treatmentwith an active compound.

Treating cancer can result in a decrease in tumor growth rate.Preferably, after treatment, tumor growth rate is reduced by at least 5%relative to number prior to treatment; more preferably, tumor growthrate is reduced by at least 10%; more preferably, reduced by at least20%; more preferably, reduced by at least 30%; more preferably, reducedby at least 40%; more preferably, reduced by at least 50%; even morepreferably, reduced by at least 50%; and most preferably, reduced by atleast 75%. Tumor growth rate may be measured by any reproducible meansof measurement. Tumor growth rate can be measured according to a changein tumor diameter per unit time.

Treating cancer can result in a decrease in tumor regrowth. Preferably,after treatment, tumor regrowth is less than 5%; more preferably, tumorregrowth is less than 10%; more preferably, less than 20%; morepreferably, less than 30%; more preferably, less than 40%; morepreferably, less than 50%; even more preferably, less than 50%; and mostpreferably, less than 75%. Tumor regrowth may be measured by anyreproducible means of measurement. Tumor regrowth is measured, forexample, by measuring an increase in the diameter of a tumor after aprior tumor shrinkage that followed treatment. A decrease in tumorregrowth is indicated by failure of tumors to reoccur after treatmenthas stopped.

Treating cancer can result in a reduction in the rate of cellularproliferation. Preferably, after treatment, the rate of cellularproliferation is reduced by at least 5%; more preferably, by at least10%; more preferably, by at least 20%; more preferably, by at least 30%;more preferably, by at least 40%; more preferably, by at least 50%; evenmore preferably, by at least 50%; and most preferably, by at least 75%.The rate of cellular proliferation may be measured by any reproduciblemeans of measurement. The rate of cellular proliferation is measured,for example, by measuring the number of dividing cells in a tissuesample per unit time.

Treating cancer can result in a reduction in the proportion ofproliferating cells. Preferably, after treatment, the proportion ofproliferating cells is reduced by at least 5%; more preferably, by atleast 10%; more preferably, by at least 20%; more preferably, by atleast 30%; more preferably, by at least 40%; more preferably, by atleast 50%; even more preferably, by at least 50%; and most preferably,by at least 75%. The proportion of proliferating cells may be measuredby any reproducible means of measurement. Preferably, the proportion ofproliferating cells is measured, for example, by quantifying the numberof dividing cells relative to the number of nondividing cells in atissue sample. The proportion of proliferating cells can be equivalentto the mitotic index.

Treating cancer can result in a decrease in size of an area or zone ofcellular proliferation. Preferably, after treatment, size of an area orzone of cellular proliferation is reduced by at least 5% relative to itssize prior to treatment; more preferably, reduced by at least 10%; morepreferably, reduced by at least 20%; more preferably, reduced by atleast 30%; more preferably, reduced by at least 40%; more preferably,reduced by at least 50%; even more preferably, reduced by at least 50%;and most preferably, reduced by at least 75%. Size of an area or zone ofcellular proliferation may be measured by any reproducible means ofmeasurement. The size of an area or zone of cellular proliferation maybe measured as a diameter or width of an area or zone of cellularproliferation.

Treating cancer can result in a decrease in the number or proportion ofcells having an abnormal appearance or morphology. Preferably, aftertreatment, the number of cells having an abnormal morphology is reducedby at least 5% relative to its size prior to treatment; more preferably,reduced by at least 10%; more preferably, reduced by at least 20%; morepreferably, reduced by at least 30%; more preferably, reduced by atleast 40%; more preferably, reduced by at least 50%; even morepreferably, reduced by at least 50%; and most preferably, reduced by atleast 75%. An abnormal cellular appearance or morphology may be measuredby any reproducible means of measurement. An abnormal cellularmorphology can be measured by microscopy, e.g., using an inverted tissueculture microscope. An abnormal cellular morphology can take the form ofnuclear pleiomorphism.

Treating cancer can result in cell death, and preferably, cell deathresults in a decrease of at least 10% in number of cells in apopulation. More preferably, cell death means a decrease of at least20%; more preferably, a decrease of at least 30%; more preferably, adecrease of at least 40%; more preferably, a decrease of at least 50%;most preferably, a decrease of at least 75%. Number of cells in apopulation may be measured by any reproducible means. A number of cellsin a population can be measured by fluorescence activated cell sorting(FACS), immunofluorescence microscopy and light microscopy. Methods ofmeasuring cell death are as shown in Li et al., Proc Natl Acad Sci USA.100(5): 2674-8, 2003. In an aspect, cell death occurs by apoptosis.

As used herein, the term “selectively” means tending to occur at ahigher frequency in one population than in another population. Thecompared populations can be cell populations. Preferably, a compound ofthe present invention, or a pharmaceutically acceptable salt, polymorphor solvate thereof, acts selectively on a cancer or precancerous cellbut not on a normal cell. Preferably, a compound of the presentinvention, or a pharmaceutically acceptable salt, polymorph or solvatethereof, acts selectively to modulate one molecular target (e.g., atarget protein methyltransferase) but does not significantly modulateanother molecular target (e.g., a non-target protein methyltransferase).The invention also provides a method for selectively inhibiting theactivity of an enzyme, such as a protein methyltransferase. Preferably,an event occurs selectively in population A relative to population B ifit occurs greater than two times more frequently in population A ascompared to population B. An event occurs selectively if it occursgreater than five times more frequently in population A. An event occursselectively if it occurs greater than ten times more frequently inpopulation A; more preferably, greater than fifty times; even morepreferably, greater than 100 times; and most preferably, greater than1000 times more frequently in population A as compared to population B.For example, cell death would be said to occur selectively in cancercells if it occurred greater than twice as frequently in cancer cells ascompared to normal cells.

A compound of the present invention, or a pharmaceutically acceptablesalt, polymorph or solvate thereof, can modulate the activity of amolecular target (e.g., a target protein methyltransferase). Modulatingrefers to stimulating or inhibiting an activity of a molecular target.Preferably, a compound of the present invention, or a pharmaceuticallyacceptable salt, polymorph or solvate thereof, modulates the activity ofa molecular target if it stimulates or inhibits the activity of themolecular target by at least 2-fold relative to the activity of themolecular target under the same conditions but lacking only the presenceof said compound. More preferably, a compound of the present invention,or a pharmaceutically acceptable salt, polymorph or solvate thereof,modulates the activity of a molecular target if it stimulates orinhibits the activity of the molecular target by at least 5-fold, atleast 10-fold, at least 20-fold, at least 50-fold, at least 100-foldrelative to the activity of the molecular target under the sameconditions but lacking only the presence of said compound. The activityof a molecular target may be measured by any reproducible means. Theactivity of a molecular target may be measured in vitro or in vivo. Forexample, the activity of a molecular target may be measured in vitro byan enzymatic activity assay or a DNA binding assay, or the activity of amolecular target may be measured in vivo by assaying for expression of areporter gene.

A compound of the present invention, or a pharmaceutically acceptablesalt, polymorph or solvate thereof, does not significantly modulate theactivity of a molecular target if the addition of the compound does notstimulate or inhibit the activity of the molecular target by greaterthan 10% relative to the activity of the molecular target under the sameconditions but lacking only the presence of said compound.

As used herein, the term “isozyme selective” means preferentialinhibition or stimulation of a first isoform of an enzyme in comparisonto a second isoform of an enzyme (e.g., preferential inhibition orstimulation of a protein methyltransferase isozyme alpha in comparisonto a protein methyltransferase isozyme beta). Preferably, a compound ofthe present invention, or a pharmaceutically acceptable salt, polymorphor solvate thereof, demonstrates a minimum of a fourfold differential,preferably a tenfold differential, more preferably a fifty folddifferential, in the dosage required to achieve a biological effect.Preferably, a compound of the present invention, or a pharmaceuticallyacceptable salt, polymorph or solvate thereof, demonstrates thisdifferential across the range of inhibition, and the differential isexemplified at the IC₅₀, i.e., a 50% inhibition, for a molecular targetof interest.

Administering a compound of the present invention, or a pharmaceuticallyacceptable salt, polymorph or solvate thereof, to a cell or a subject inneed thereof can result in modulation (i.e., stimulation or inhibition)of an activity of a protein methyltransferase of interest.

Detection of methylation of H3-K27, formation of trimethylated H3-K27,conversion of monomethylated H3-K27 to dimethylated H3-K27, orconversion of dimethylated H3-K27 to trimethylated H3-K27 can beaccomplished using any suitable method. Exemplary methods can be foundin US20120071418, the contents of which are incorporated herein byreference.

Administering a compound of the present invention, or a pharmaceuticallyacceptable salt, polymorph or solvate thereof, to a cell or a subject inneed thereof results in modulation (i.e., stimulation or inhibition) ofan activity of an intracellular target (e.g., substrate). Severalintracellular targets can be modulated with the compounds of the presentinvention, including, but not limited to, protein methyltrasferase.

Preferably, an effective amount of a compound of the present invention,or a pharmaceutically acceptable salt, polymorph or solvate thereof, isnot significantly cytotoxic to normal cells. A therapeutically effectiveamount of a compound is not significantly cytotoxic to normal cells ifadministration of the compound in a therapeutically effective amountdoes not induce cell death in greater than 10% of normal cells. Atherapeutically effective amount of a compound does not significantlyaffect the viability of normal cells if administration of the compoundin a therapeutically effective amount does not induce cell death ingreater than 10% of normal cells. In an aspect, cell death occurs byapoptosis.

Contacting a cell with a compound of the present invention, or apharmaceutically acceptable salt, polymorph or solvate thereof, caninduce or activate cell death selectively in cancer cells. Administeringto a subject in need thereof a compound of the present invention, or apharmaceutically acceptable salt, polymorph or solvate thereof, caninduce or activate cell death selectively in cancer cells. Contacting acell with a compound of the present invention, or a pharmaceuticallyacceptable salt, polymorph or solvate thereof, can induce cell deathselectively in one or more cells affected by a cell proliferativedisorder. Preferably, administering to a subject in need thereof acompound of the present invention, or a pharmaceutically acceptablesalt, polymorph or solvate thereof, induces cell death selectively inone or more cells affected by a cell proliferative disorder.

One skilled in the art may refer to general reference texts for detaileddescriptions of known techniques discussed herein or equivalenttechniques. These texts include Ausubel et al., Current Protocols inMolecular Biology, John Wiley and Sons, Inc. (2005); Sambrook et al.,Molecular Cloning, A Laboratory Manual (3^(rd) edition), Cold SpringHarbor Press, Cold Spring Harbor, N.Y. (2000); Coligan et al., CurrentProtocols in Immunology, John Wiley & Sons, N.Y.; Enna et al., CurrentProtocols in Pharmacology, John Wiley & Sons, N.Y.; Fingl et al., ThePharmacological Basis of Therapeutics (1975), Remington's PharmaceuticalSciences, Mack Publishing Co., Easton, Pa., 18^(th) edition (1990).These texts can, of course, also be referred to in making or using anaspect of the invention.

A compound (i.e., an EZH2 inhibitor) that can be used in any methodsdescribed herein may have the following Formula I:

or a pharmaceutically acceptable salt thereof; wherein

R⁷⁰¹ is H, F, OR⁷⁰⁷, NHR⁷⁰⁷, —(C≡C)—(CH₂)_(n7)—R⁷⁰⁸, phenyl, 5- or6-membered heteroaryl, C3-8 cycloalkyl, or 4-7 membered heterocycloalkylcontaining 1-3 heteroatoms, wherein the phenyl, 5- or 6-memberedheteroaryl, C3-8 cycloalkyl or 4-7 membered heterocycloalkyl eachindependently is optionally substituted with one or more groups selectedfrom halo, C1-3 alkyl, OH, O—C₁₋₆ alkyl, NH—C₁₋₆ alkyl, and, C₁₋₃ alkylsubstituted with C₃₋₈ cycloalkyl or 4-7 membered heterocycloalkylcontaining 1-3 heteroatoms, wherein each of the O—C₁₋₆ alkyl and NH—C₁₋₆alkyl is optionally substituted with hydroxyl, O—C₁₋₃ alkyl or NH—C₁₋₃alkyl, each of the O—C₁₋₃ alkyl and NH—C₁₋₃ alkyl being optionallyfurther substituted with O—C₁₋₃ alkyl or NH—C₁₋₃ alkyl;

each of R⁷⁰² and R⁷⁰³, independently is H, halo, C₁₋₄ alkyl, C₁₋₆alkoxyl or C₆-C₁₀ aryloxy, each optionally substituted with one or morehalo;

each of R⁷⁰⁴ and R⁷⁰⁵, independently is C₁₋₄ alkyl;

R⁷⁰⁶ is cyclohexyl substituted by N(C₁₋₄ alkyl)₂ wherein one or both ofthe C₁₋₄ alkyl is substituted with C₁₋₆ alkoxy; or R⁷⁰⁶ istetrahydropyranyl;

R⁷⁰⁷ is C₁₋₄ alkyl optionally substituted with one or more groupsselected from hydroxyl, C₁₋₄ alkoxy, amino, mono- or di-C₁₋₄ alkylamino,C₃₋₈ cycloalkyl, and 4-7 membered heterocycloalkyl containing 1-3heteroatoms, wherein the C₃₋₈ cycloalkyl or 4-7 memberedheterocycloalkyl each independently is further optionally substitutedwith C₁₋₃ alkyl;

R⁷⁰⁸ is C₁₋₄ alkyl optionally substituted with one or more groupsselected from OH, halo, and C₁₋₄ alkoxy, 4-7 membered heterocycloalkylcontaining 1-3 heteroatoms, or O—C₁₋₆ alkyl, wherein the 4-7 memberedheterocycloalkyl can be optionally further substituted with OH or C₁₋₆alkyl; and

n₇ is 0, 1 or 2.

For example, R⁷⁰⁶ is cyclohexyl substituted by N(C₁₋₄ alkyl)₂ whereinone of the C₁₋₄ alkyl is unsubstituted and the other is substituted withmethoxy.

For example, R⁷⁰⁶ is

For example, the compound is of Formula II:

For example, R⁷⁰² is methyl or isopropyl and R⁷⁰³ is methyl or methoxyl.

For example, R⁷⁰⁴ is methyl.

For example, R⁷⁰¹ is OR⁷⁰⁷ and R⁷⁰⁷ is C₁₋₃ alkyl optionally substitutedwith OCH₃ or morpholine.

For example, R⁷⁰¹ is H or F.

For example, R⁷⁰¹ is tetrahydropyranyl, phenyl, pyridyl, pyrimidyl,pyrazinyl, imidazolyl, or pyrazolyl, each of which is optionallysubstituted with methyl, methoxy, ethyl substituted with morpholine, or—OCH₂CH₂OCH₃.

For example, R⁷⁰⁸ is morpholine, piperidine, piperazine, pyrrolidine,diazepane, or azetidine, each of which is optionally substituted with OHor C₁₋₆ alkyl.

For example, R⁷⁰⁸ is morpholine

For example, R⁷⁰⁸ is piperazine substituted with C₁₋₆ alkyl.

For example, R⁷⁰⁸ is methyl, t-butyl or C(CH₃)₂OH.

A compound (i.e., an EZH2 inhibitor) that can be used in any methodsdescribed herein may have the following Formula III:

or a pharmaceutically acceptable salt thereof.

In this formula:

R⁸⁰¹ is C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₈ cycloalkyl, 4-7membered heterocycloalkyl containing 1-3 heteroatoms, phenyl or 5- or6-membered heteroaryl, each of which is substituted with O—C₁₋₆alkyl-R_(x) or NH—C₁₋₆ alkyl-R_(x), wherein R_(x) is hydroxyl, O—C₁₋₃alkyl or NH—C₁₋₃ alkyl, and R_(x) is optionally further substituted withO—C₁₋₃ alkyl or NH—C₁₋₃ alkyl except when R_(x) is hydroxyl; or R⁸⁰¹ isphenyl substituted with -Q₂-T₂, wherein Q₂ is a bond or C₁-C₃ alkyllinker optionally substituted with halo, cyano, hydroxyl or C₁-C₆alkoxy, and T₂ is optionally substituted 4- to 12-memberedheterocycloalkyl; and R⁸⁰¹ is optionally further substituted;

each of R⁸⁰² and R⁸⁰³, independently is H, halo, C₁₋₄ alkyl, C₁₋₆alkoxyl or C₆-C₁₀ aryloxy, each optionally substituted with one or morehalo;

each of R⁸⁰⁴ and R⁸⁰⁵, independently is C₁₋₄ alkyl; and

R⁸⁰⁶ is -Q_(x)-T_(x), wherein Q_(x) is a bond or C₁₋₄ alkyl linker,T_(x) is H, optionally substituted C₁₋₄ alkyl, optionally substitutedC₃-C₈ cycloalkyl or optionally substituted 4- to 14-memberedheterocycloalkyl.

For example, each of Q_(x) and Q₂ independently is a bond or methyllinker, and each of T_(x) and T₂ independently is tetrahydropyranyl,piperidinyl substituted by 1, 2, or 3 C₁₋₄ alkyl groups, or cyclohexylsubstituted by N(C₁₋₄ alkyl)₂ wherein one or both of the C₁₋₄ alkyl isoptionally substituted with C₁₋₆ alkoxy;

For example, R⁸⁰⁶ is cyclohexyl substituted by N(C₁₋₄ alkyl)₂ or R⁸⁰⁶ istetrahydropyranyl.

For example, R⁸⁰⁶ is

For example, R⁸⁰¹ is phenyl or 5- or 6-membered heteroaryl substitutedwith O—C₁₋₆ alkyl-R_(x), or R⁸⁰¹ is phenylsubstituted withCH₂-tetrahydropyranyl.

For example, a compound of the present invention is of Formula IVa orIVb:

wherein Z′ is CH or N, and R⁸⁰⁷ is C₂₋₃ alkyl-R_(x).

For example, R⁸⁰⁷ is —CH₂CH₂OH, —CH₂CH₂OCH₃, or —CH₂CH₂OCH₂CH₂OCH₃.

For example, R⁸⁰² is methyl or isopropyl and R⁸⁰³ is methyl or methoxyl.

For example, R⁸⁰⁴ is methyl.

A compound of the present invention may have the following Formula (V):

or a pharmaceutically acceptable salt or ester thereof.

In this formula:

R², R⁴ and R¹² are each independently C₁₋₆ alkyl;

R⁶ is C₆-C₁₀ aryl or 5- or 6-membered heteroaryl, each of which isoptionally substituted with one or more -Q₂-T₂, wherein Q₂ is a bond orC₁-C₃ alkyl linker optionally substituted with halo, cyano, hydroxyl orC₁-C₆ alkoxy, and T₂ is H, halo, cyano, —OR_(a), —NR_(a)R_(b),—(NR_(a)R_(b)R_(c))⁺A⁻, —C(O)R_(a), —C(O)OR_(a), —C(O)NR_(a)R_(b),—NR_(b)C(O)R_(a), —NR_(b)C(O)OR_(a),—S(O)₂R_(a), —S(O)₂NR_(a)R_(b), orR_(S2), in which each of R_(a), R_(b), and R_(c), independently is H orR_(S3), A⁻ is a pharmaceutically acceptable anion, each of R_(S2) andR_(S3), independently, is C₁-C₆ alkyl, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4to 12-membered heterocycloalkyl, or 5- or 6-membered heteroaryl, orR_(a) and R_(b), together with the N atom to which they are attached,form a 4 to 12-membered heterocycloalkyl ring having 0 or 1 additionalheteroatom, and each of R_(S2), R_(S3), and the 4 to 12-memberedheterocycloalkyl ring formed by R_(a) and R_(b), is optionallysubstituted with one or more -Q₃-T₃, wherein Q₃ is a bond or C₁-C₃ alkyllinker each optionally substituted with halo, cyano, hydroxyl or C₁-C₆alkoxy, and T₃ is selected from the group consisting of halo, cyano,C₁-C₆ alkyl, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-memberedheterocycloalkyl, 5- or 6-membered heteroaryl, OR_(d), COOR_(d),—S(O)₂R_(d), —NR_(d)R_(e), and —C(O)NR_(d)R_(e), each of R_(d) and R_(e)independently being H or C₁-C₆ alkyl, or -Q₃-T₃ is oxo; or any twoneighboring -Q₂-T₂, together with the atoms to which they are attachedform a 5- or 6-membered ring optionally containing 1-4 heteroatomsselected from N, O and S and optionally substituted with one or moresubstituents selected from the group consisting of halo, hydroxyl, COOH,C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino,di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-memberedheterocycloalkyl, and 5- or 6-membered heteroaryl;

R₇ is -Q₄-T₄, in which Q₄ is a bond, C₁-C₄ alkyl linker, or C₂-C₄alkenyl linker, each linker optionally substituted with halo, cyano,hydroxyl or C₁-C₆ alkoxy, and T₄ is H, halo, cyano, NR_(f)R_(g),—OR_(f), —C(O)R_(f), —C(O)OR_(f), —C(O)NR_(f)R_(g), —C(O)NR_(f)OR_(g),—NR_(f)C(O)R_(g), —S(O)₂R_(f), or R_(S4), in which each of R_(f) andR_(g), independently is H or R_(S5), each of R_(S4) and R_(S5),independently is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or6-membered heteroaryl, and each of R_(S4) and R_(S5) is optionallysubstituted with one or more -Q₅-T₅, wherein Q₅ is a bond, C(O),C(O)NR_(k), NR_(k)C(O), S(O)₂, or C₁-C₃ alkyl linker, R_(k) being H orC₁-C₆ alkyl, and T₅ is H, halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, 5- or6-membered heteroaryl, or S(O)_(q)R_(q) in which q is 0, 1, or 2 andR_(q) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈ cycloalkyl,C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-memberedheteroaryl, and T₅ is optionally substituted with one or moresubstituents selected from the group consisting of halo, C₁-C₆ alkyl,hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-memberedheterocycloalkyl, and 5- or 6-membered heteroaryl except when T₅ is H,halo, hydroxyl, or cyano; or -Q₅-T₅ is oxo; and

R₈ is H, halo, hydroxyl, COOH, cyano, R_(S6), OR_(S6), or COOR_(S6), inwhich R_(S6) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈cycloalkyl, 4 to 12-membered heterocycloalkyl, amino, mono-C₁-C₆alkylamino, or di-C₁-C₆ alkylamino, and R_(S6) is optionally substitutedwith one or more substituents selected from the group consisting ofhalo, hydroxyl, COOH, C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆ alkoxyl, amino,mono-C₁-C₆ alkylamino, and di-C₁-C₆ alkylamino; or R₇ and R₈, togetherwith the N atom to which they are attached, form a 4 to 11-memberedheterocycloalkyl ring having 0 to 2 additional heteroatoms, and the 4 to11-membered heterocycloalkyl ring formed by R₇ and R₈ is optionallysubstituted with one or more -Q₆-T₆, wherein Q₆ is a bond, C(O),C(O)NR_(m), NR_(m)C(O), S(O)₂, or C₁-C₃ alkyl linker, R_(m) being H orC₁-C₆ alkyl, and T₆ is H, halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈cycloalkyl, C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, 5- or6-membered heteroaryl, or S(O)_(p)R_(p) in which p is 0, 1, or 2 andR_(p) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈ cycloalkyl,C₆-C₁₀ aryl, 4 to 12-membered heterocycloalkyl, or 5- or 6-memberedheteroaryl, and T₆ is optionally substituted with one or moresubstituents selected from the group consisting of halo, C₁-C₆ alkyl,hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-memberedheterocycloalkyl, and 5- or 6-membered heteroaryl except when T₆ is H,halo, hydroxyl, or cyano; or -Q₆-T₆ is oxo.

For example, R⁶ is C₆-C₁₀ aryl or 5- or 6-membered heteroaryl, each ofwhich is optionally, independently substituted with one or more -Q₂-T₂,wherein Q₂ is a bond or C₁-C₃ alkyl linker, and T₂ is H, halo, cyano,—OR_(a), —NR_(a)R_(b), —(NR_(a)R_(b)R_(c))⁺A⁻, —C(O)NR_(a)R_(b),—NR_(b)C(O)R_(a), —S(O)₂R_(a), or R_(S2), in which each of R_(a) andR_(b), independently is H or R_(S3), each of R_(S2) and R_(S3),independently, is C₁-C₆ alkyl, or R_(a) and R_(b), together with the Natom to which they are attached, form a 4 to 7-membered heterocycloalkylring having 0 or 1 additional heteroatom, and each of R_(S2), R_(S3),and the 4 to 7-membered heterocycloalkyl ring formed by R_(a) and R_(b),is optionally, independently substituted with one or more -Q₃-T₃,wherein Q₃ is a bond or C₁-C₃ alkyl linker and T₃ is selected from thegroup consisting of halo, C₁-C₆ alkyl, 4 to 7-membered heterocycloalkyl,OR_(d), —S(O)₂R_(d), and —NR_(d)R_(e), each of R_(d) and R_(e)independently being H or C₁-C₆ alkyl, or -Q₃-T₃ is oxo; or any twoneighboring -Q₂-T₂, together with the atoms to which they are attachedform a 5- or 6-membered ring optionally containing 1-4 heteroatomsselected from N, O and S.

For example, the compound of the present invention is of Formula (VI):

or a pharmaceutically acceptable salt thereof, wherein Q₂ is a bond ormethyl linker, T₂ is H, halo, —OR_(a), —NR_(a)R_(b),—(NR_(a)R_(b)R_(c))⁺A⁻, or —S(O)₂NR_(a)R_(b), R₇ is piperidinyl,tetrahydropyran, cyclopentyl, or cyclohexyl, each optionally substitutedwith one -Q₅-T₅ and R₈ is ethyl.

A compound of the present invention may have the following Formula(VIa):

wherein each of R_(a) and R_(b), independently is H or R_(S3), R_(S3)being C₁-C₆ alkyl, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 12-memberedheterocycloalkyl, or 5- or 6-membered heteroaryl, or R_(a) and R_(b),together with the N atom to which they are attached, form a 4 to12-membered heterocycloalkyl ring having 0 or 1 additional heteroatom,and each of R_(S3) and the 4 to 12-membered heterocycloalkyl ring formedby R_(a) and R_(b), is optionally substituted with one or more -Q₃-T₃,wherein Q₃ is a bond or C₁-C₃ alkyl linker each optionally substitutedwith halo, cyano, hydroxyl or C₁-C₆ alkoxy, and T₃ is selected from thegroup consisting of halo, cyano, C₁-C₆ alkyl, C₃-C₈ cycloalkyl, C₆-C₁₀aryl, 4 to 12-membered heterocycloalkyl, 5- or 6-membered heteroaryl,OR_(a), COOR_(d), —S(O)₂R_(d), —NR_(d)R_(e), and —C(O)NR_(d)R_(e), eachof R_(d) and R_(e) independently being H or C₁-C₆ alkyl, or -Q₃-T₃ isoxo;

R₇ is -Q₄-T₄, in which Q₄ is a bond, C₁-C₄ alkyl linker, or C₂-C₄alkenyl linker, each linker optionally substituted with halo, cyano,hydroxyl or C₁-C₆ alkoxy, and T₄ is H, halo, cyano, NR_(f)R_(g),—OR_(f), —C(O)R_(f), —C(O)OR_(f), —C(O)NR_(f)R_(g), —C(O)NR_(f)OR_(g),—NR_(f)C(O)R_(g), —S(O)₂R_(f), or R_(S4), in which each of R_(f) andR_(g), independently is H or R_(S5), each of R_(S4) and R_(S5),independently is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈cycloalkyl, C₆-C₁₀ aryl, 4 to 7-membered heterocycloalkyl, or 5- or6-membered heteroaryl, and each of R_(S4) and R_(S5) is optionallysubstituted with one or more -Q₅-T₅, wherein Q₅ is a bond, C(O),C(O)NR_(k), NR_(k)C(O), S(O)₂, or C₁-C₃ alkyl linker, R_(k) being H orC₁-C₆ alkyl, and T₅ is H, halo, C₁-C₆ alkyl, hydroxyl, cyano, C₁-C₆alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆ alkylamino, C₃-C₈cycloalkyl, C₆-C₁₀ aryl, 4 to 7-membered heterocycloalkyl, 5- or6-membered heteroaryl, or S(O)_(q)R_(q) in which q is 0, 1, or 2 andR_(q) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, C₃-C₈cycloalkyl,C₆-C₁₀ aryl, 4 to 7-membered heterocycloalkyl, or 5- or 6-memberedheteroaryl, and T₅ is optionally substituted with one or moresubstituents selected from the group consisting of halo, C₁-C₆ alkyl,hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino, di-C₁-C₆alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 7-memberedheterocycloalkyl, and 5- or 6-membered heteroaryl except when T₅ is H,halo, hydroxyl, or cyano; or -Q₅-T₅ is oxo; provided that R₇ is not H;and

R₈ is H, halo, hydroxyl, COOH, cyano, R_(S6), OR_(S6), or COOR_(S6), inwhich R_(S6) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl, amino,mono-C₁-C₆ alkylamino, or di-C₁-C₆ alkylamino, and R_(S6) is optionallysubstituted with one or more substituents selected from the groupconsisting of halo, hydroxyl, COOH, C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆alkoxyl, amino, mono-C₁-C₆ alkylamino, and di-C₁-C₆ alkylamino; or R₇and R₈, together with the N atom to which they are attached, form a 4 to11-membered heterocycloalkyl ring which has 0 to 2 additionalheteroatoms and is optionally substituted with one or more -Q₆-T₆,wherein Q₆ is a bond, C(O), C(O)NR_(m), NR_(m)C(O), S(O)₂, or C₁-C₃alkyl linker, R_(m) being H or C₁-C₆ alkyl, and T₆ is H, halo, C₁-C₆alkyl, hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino,di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 7-memberedheterocycloalkyl, 5- or 6-membered heteroaryl, or S(O)_(p)R_(p) in whichp is 0, 1, or 2 and R_(p) is C₁-C₆ alkyl, C₂-C₆ alkenyl, C₂-C₆ alkynyl,C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 7-membered heterocycloalkyl, or 5-or 6-membered heteroaryl, and T₆ is optionally substituted with one ormore substituents selected from the group consisting of halo, C₁-C₆alkyl, hydroxyl, cyano, C₁-C₆ alkoxyl, amino, mono-C₁-C₆ alkylamino,di-C₁-C₆ alkylamino, C₃-C₈ cycloalkyl, C₆-C₁₀ aryl, 4 to 7-memberedheterocycloalkyl, and 5- or 6-membered heteroaryl except when T₆ is H,halo, hydroxyl, or cyano; or -Q₆-T₆ is oxo.

For example, R_(a) and R_(b), together with the N atom to which they areattached, form a 4 to 7-membered heterocycloalkyl ring having 0 or 1additional heteroatoms to the N atom and the ring is optionallysubstituted with one or more -Q₃-T₃, wherein the heterocycloalkyl isazetidinyl, pyrrolidinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl,isoxazolidinyl, triazolidinyl, piperidinyl, 1,2,3,6-tetrahydropyridinyl,piperazinyl, or morpholinyl.

For example, R₇ is C₃-C₈ cycloalkyl or 4 to 7-membered heterocycloalkyl,each optionally substituted with one or more -Q₅-T₅.

For example, R₇ is piperidinyl, tetrahydropyran,tetrahydro-2H-thiopyranyl, cyclopentyl, cyclohexyl, pyrrolidinyl, orcycloheptyl, each optionally substituted with one or more -Q₅-T₅.

For example, R₈ is H or C₁-C₆ alkyl which is optionally substituted withone or more substituents selected from the group consisting of halo,hydroxyl, COOH, C(O)O—C₁-C₆ alkyl, cyano, C₁-C₆ alkoxyl, amino,mono-C₁-C₆ alkylamino, and di-C₁-C₆ alkylamino.

In some embodiments, a compound that can be used in any methodspresented here is:

stereoisomers thereof or pharmaceutically acceptable salt or solvatethereof.

In some embodiments, a compound that can be used in any methodspresented here is:

stereoisomers thereof or pharmaceutically acceptable salts and solvatesthereof.

In some embodiments, a compound that can be used in any methodspresented here is:

stereoisomers thereof or pharmaceutically acceptable salts and solvatesthereof.

In some embodiments, the compounds suitable for use in the method ofthis invention include compounds of Formula (VII):

wherein,

V¹ is N or CR⁷,

V² is N or CR², provided when V¹ is N, V² is N,

X and Z are selected independently from the group consisting ofhydrogen, (C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, unsubstituted orsubstituted (C₃-C₈)cycloalkyl, unsubstituted or substituted(C₃-C₈)cycloalkyl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl, unsubstituted orsubstituted (C₅-C₈)cycloalkenyl, unsubstituted or substituted(C₅-C₈)cycloalkenyl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl,(C₆-C₁₀)bicycloalkyl, unsubstituted or substituted heterocycloalkyl,unsubstituted or substituted heterocycloalkyl-(C₁-C₈)alkyl or—(C₂-C₈)alkenyl, unsubstituted or substituted aryl, unsubstituted orsubstituted aryl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl, unsubstituted orsubstituted heteroaryl, unsubstituted or substitutedheteroaryl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl, halo, cyano,

—COR^(a),—CO₂R^(a), —CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b), —SR^(a),—SOR^(a), —SO₂R^(a), —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b),—NR^(a)C(O)R^(b), —NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a),—NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b),—NR^(a)NR^(a)C(O)R^(b), —NR^(a)NR^(a)C(O)NR^(a)R^(b),—NR^(a)NR^(a)C(O)OR^(a), —OR^(a), —OC(O)R^(a), and —OC(O)NR^(a)R^(b);

Y is H or halo;

R¹ is (C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, unsubstituted orsubstituted (C₃-C₈)cycloalkyl, unsubstituted or substituted(C₃-C₈)cycloalkyl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl, unsubstituted orsubstituted (C₅-C₈)cycloalkenyl, unsubstituted or substituted(C₅-C₈)cycloalkenyl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl, unsubstituted orsubstituted (C₆-C₁₀)bicycloalkyl, unsubstituted or substitutedheterocycloalkyl or —(C₂-C₈)alkenyl, unsubstituted or substitutedheterocycloalkyl-(C₁-C₈)alkyl, unsubstituted or substituted aryl,unsubstituted or substituted aryl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl,unsubstituted or substituted heteroaryl, unsubstituted or substitutedheteroaryl-(C₁-C₈)alkyl or —(C₂-C₈)alkenyl, —COR^(a), —CO₂R_(a),—CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b);

R² is hydrogen, (C₁-C₈)alkyl, trifluoromethyl, alkoxy, or halo, in whichsaid (C₁-C₈)alkyl is optionally substituted with one to two groupsselected from amino and (C₁-C₃)alkylamino;

R₇ is hydrogen, (C₁-C₃)alkyl, or alkoxy;

R³ is hydrogen, (C₁-C₈)alkyl, cyano, trifluoromethyl, —NR^(a)R^(b), orhalo;

R⁶ is selected from the group consisting of hydrogen, halo,(C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, unsubstituted orsubstituted (C₃-C₈)cycloalkyl, unsubstituted or substituted(C₃-C₈)cycloalkyl-(C₁-C₈)alkyl, unsubstituted or substituted(C₅-C₈)cycloalkenyl, unsubstituted or substituted(C₅-C₈)cycloalkenyl(C₁-C₈)alkyl, (C₆-C₁₀)bicycloalkyl, unsubstituted orsubstituted heterocycloalkyl, unsubstituted or substitutedheterocycloalkyl-(C₁—C₈)alkyl, unsubstituted or substituted aryl,unsubstituted or substituted aryl-(C₁-C₈)alkyl, unsubstituted orsubstituted heteroaryl, unsubstituted or substitutedheteroaryl-(C₁-C₈)alkyl, cyano, —COR^(a), —CO₂R_(a),

—CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b), —SR^(a), —SOR^(a), —SO₂R_(a),—SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b),—NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b),—NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b), —NR^(a)NR^(a)C(O)R^(b),—NR^(a)NR^(a)C(O)NR^(a)R^(b), —NR^(a)NR^(a)C(O)OR^(a), —OR^(a),—OC(O)R^(a), —OC(O)NR^(a)R^(b);

wherein any (C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, cycloalkyl,cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl groupis optionally substituted by 1, 2 or 3 groups independently selectedfrom the group consisting of —O(C₁-C₆)alkyl(R_(c))₁₋₂,—S(C₁-C₆)alkyl(R_(c))₁₋₂, —(C₁-C₆)alkyl(R_(c))₁₋₂,—(C₁-C₈)alkyl-heterocycloalkyl, (C₃-C₈)cycloalkyl-heterocycloalkyl,halo, (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl,(C₁-C₆)haloalkyl, cyano, —COR^(a), —CO₂R_(a),—CONR^(a)R^(b), —SR^(a),—SOR^(a), —SO₂R_(a), —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b),—NR^(a)C(O)R^(b), —NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR_(a),—NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b), —OR^(a), —OC(O)R^(a),OC(O)NR^(a)R^(b), heterocycloalkyl, aryl, heteroaryl, aryl(C₁-C₄)alkyl,and heteroaryl(C₁-C₄)alkyl;

-   -   wherein any aryl or heteroaryl moiety of said aryl, heteroaryl,        aryl(C₁-C₄)alkyl, or heteroaryl(C₁-C₄)alkyl is optionally        substituted by 1, 2 or 3 groups independently selected from the        group consisting of halo, (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl,        (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano, —COR^(a),        —CO₂R^(a), —CONR^(a)R^(b),—SR^(a),    -   SOR^(a), —SO₂R^(a), —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b),        —NR^(a)C(O)R^(b),—NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR_(a),        —NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b), —OR^(a), —OC(O)R_(a),        and —OC(O)NR^(a)R^(b);

R^(a) and R^(b) are each independently hydrogen, (C₁-C₈)alkyl,(C₂-C₈)alkenyl, (C₂-C₈)alkynyl, (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl,(C₆-C₁₀)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, whereinsaid (C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, cycloalkyl,cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl groupis optionally substituted by 1, 2 or 3 groups independently selectedfrom halo, hydroxyl, (C₁-C₄)alkoxy, amino, (C₁-C₄)alkylamino,((C₁-C₄)alkyl)((C₁-C₄)alkyl)amino, —CO₂H, —CO₂(C₁-C₄)alkyl,—CONH₂,—CONH(C₁-C₄)alkyl,

—CON((C₁-C₄)alkyl)((C₁-C₄)alkyl), —SO₂(C₁-C₄)alkyl,—SO₂NH₂,—SO₂NH(C₁-C₄)alkyl, and SO₂N((C₁-C₄)alkyl)((C₁-C₄)alkyl);

or R^(a) and R^(b) taken together with the nitrogen to which they areattached represent a 5-8 membered saturated or unsaturated ring,optionally containing an additional heteroatom selected from oxygen,nitrogen, and sulfur, wherein said ring is optionally substituted by 1,2 or 3 groups independently selected from (C₁-C₄)alkyl,(C₁-C₄)haloalkyl, amino, (C₁-C₄)alkylamino,((C₁-C₄)alkyl)((C₁-C₄)alkyl)amino, hydroxyl, oxo, (C₁-C₄)alkoxy, and(C₁-C₄)alkoxy(C₁-C₄)alkyl, wherein said ring is optionally fused to a(C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;

or R^(a) and R^(b) taken together with the nitrogen to which they areattached represent a 6- to 10-membered bridged bicyclic ring systemoptionally fused to a (C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, orheteroaryl ring;

each R^(c) is independently (C₁-C₄)alkylamino, —NR^(a)SO₂R^(b),—SOR^(a), —SO₂R^(a), —NR^(a)C(O)OR^(a), —NR^(a)R^(b), or —CO₂R^(a);

or a salt thereof.

Subgroups of the compounds encompassed by the general structure ofFormula (I) are represented as follows:

Subgroup A of Formula (VII)

X and Z are selected from the group consisting of (C₁-C₈)alkyl,(C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, heteroaryl, —NR^(a)R^(b), and—OR^(a);

Y is H or F;

R¹ is selected from the group consisting of (C₁-C₈)alkyl,(C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, and heteroaryl;

R² is hydrogen, (C₁-C₈)alkyl, trifluoromethyl, alkoxy, or halo, in whichsaid (C₁-C₈)alkyl is optionally substituted with one to two groupsselected from amino and (C₁-C₃)alkylamino;

R⁷ is hydrogen, (C₁-C₃)alkyl, or alkoxy;

R³ is selected from the group consisting of hydrogen, (C₁-C₈)alkyl,cyano, trifluoromethyl,—NR^(a)R^(b), and halo;

R⁶ is selected from the group consisting of hydrogen, halo, cyano,trifluoromethyl, amino, (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, aryl,heteroaryl, acylamino; (C₂-C₈)alkynyl, arylalkynyl, heteroarylalkynyl;—SO₂R^(a); —SO₂NR^(a)R^(b) and —NR^(a)SO₂R^(b);

-   -   wherein any (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, (C₂-C₈)alkynyl,        arylalkynyl, heteroarylalkynyl group is optionally substituted        by 1, 2 or 3 groups independently selected from        —O(C₁-C₆)alkyl(R^(c))₁₋₂, —S(C₁-C₆)alkyl(R^(c))₁₋₂,        —(C₁-C₆)alkyl(R^(c))i-2, —(C₁-C₈)alkyl-heterocycloalkyl,        (C₃-C₈)cycloalkyl-heterocycloalkyl, halo, (C₁-C₆)alkyl,        (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano,        —COR^(a), —CO₂R^(a), —CONR^(a)R^(b), —SR′, —SOW, —SO₂R^(a),        —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b),        —NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a),        —NR^(a)SO₂R^(b),—NR^(a)SO₂NR^(a)R^(b), —OR^(a), —OC(O)R^(a),        —OC(O)NR^(a)R^(b), heterocycloalkyl, aryl, heteroaryl,        aryl(C₁-C₄)alkyl, and heteroaryl(C₁-C₄)alkyl;

R^(a) and R^(b) are each independently hydrogen, (C₁-C₈)alkyl,(C₂-C₈)alkenyl, (C₂-C₈)alkynyl, (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl,(C₆-C₁₀)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, whereinsaid (C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, cycloalkyl,cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl groupis optionally substituted by 1, 2 or 3 groups independently selectedfrom halo, hydroxyl, (C₁-C₄)alkoxy, amino, (C₁-C₄)alkylamino,((C₁-C₄)alkyl)((C₁-C₄)alkyl)amino, —CO₂H, —CO₂(C₁-C₄)alkyl, —CONH₂,—CONH(C₁-C₄)alkyl, —CON((C₁-C₄)alkyl)((C₁-C₄)alkyl), —SO₂(C₁-C₄)alkyl,—SO₂NH₂,—SO₂NH(C₁-C₄)alkyl, and

—SO₂N((C₁-C₄)alkyl)((C₁-C₄)alkyl);

or R^(a) and R^(b) taken together with the nitrogen to which they areattached represent a 5-8 membered saturated or unsaturated ring,optionally containing an additional heteroatom selected from oxygen,nitrogen, and sulfur, wherein said ring is optionally substituted by 1,2 or 3 groups independently selected from (C₁-C₄)alkyl,(C₁-C₄)haloalkyl, amino, (C₁-C₄)alkylamino,((C₁-C₄)alkyl)((C₁-C₄)alkyl)amino, hydroxyl, oxo, (C₁-C₄)alkoxy, and(C₁-C₄)alkoxy(C₁-C₄)alkyl, wherein said ring is optionally fused to a(C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;

or R^(a) and R^(b) taken together with the nitrogen to which they areattached represent a 6- to 10-membered bridged bicyclic ring systemoptionally fused to a (C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, orheteroaryl ring. An aryl or heteroaryl group in this particular subgroupA is selected independently from the group consisting of furan,thiophene, pyrrole, oxazole, thiazole, imidazole, pyrazole, oxadiazole,thiadiazole, triazole, tetrazole, benzofuran, benzothiophene,benzoxazole, benzothiazole, phenyl, pyridine, pyridazine, pyrimidine,pyrazine, triazine, tetrazine, quinoline, cinnoline, quinazoline,quinoxaline, and naphthyridine or another aryl or heteroaryl group asfollows:

wherein in (1),

A is O, NH, or S; B is CH or N, and C is hydrogen or C₁-C₈ alkyl; or

wherein in (2),

D is N or C optionally substituted by hydrogen or C₁-C₈ alkyl; or

wherein in (3),

E is NH or CH₂; F is O or CO; and G is NH or CH₂; or

wherein in (4),

J is O, S or CO; or

wherein in (5),

Q is CH or N;

M is CH or N; and

L/(5) is hydrogen, halo, amino, cyano, (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl,—COR^(a), —CO₂R^(a), —CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b), —SO₂R^(a),—SO₂NR^(a)R^(b), —NR^(a)R^(b), —NR^(a)C(O)R^(b),—NR^(a)SO₂R^(b),—NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b), —NR^(a)NR^(a)C(O)R^(b),—NR^(a)NR^(a)C(O)NR^(a)R^(b), or —OR^(a),

-   -   wherein any (C₁-C₈)alkyl or (C₃-C₈)cycloalkyl group is        optionally substituted by 1, 2 or 3 groups independently        selected from (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl,        (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano, —COR^(a),        —CO₂R^(a), —CONR^(a)R^(b), —SR^(a), —SOR^(a), —SO₂R^(a),        —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b),        —NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b),        —NR^(a)SO₂NR^(a)R^(b), —OR^(a), —OC(O)R^(a), and        —OC(O)NR_(a)R^(b); wherein R^(a) and R^(b) are defined as above;        or

wherein in (6),

L/(6) is NH or CH₂; or

wherein in 7,

-   -   M/(7) is hydrogen, halo, amino, cyano, (C₁-C₈)alkyl,        (C₃-C₈)cycloalkyl, heterocycloalkyl, —COR^(a), —CO₂R^(a),        —CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b), —SO₂R^(a),        —SO₂NR^(a)R^(b), —NR^(a)R^(b), —NR^(a)C(O)R^(b),        —NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b),        —NR^(a)NR^(a)C(O)R^(b), —NR^(a)NR^(a)C(O)NR^(a)R^(b), or        —OR^(a),    -   wherein any (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, or heterocycloalkyl        group is optionally substituted by 1, 2 or 3 groups        independently selected from (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl,        (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano, —COR^(a),        —CO₂R^(a), —CONR^(a)R^(b), —SR^(a), —SOR^(a), —SO₂R^(a),        —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b),        —NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b),        —NR^(a)SO₂NR^(a)R^(b), —OR^(a), —OC(O)R^(a), and        —OC(O)NR^(a)R^(b); wherein R^(a) and R^(b) are defined as above;        or

wherein in (8),

P is CH₂, NH, O, or S; Q/(8) is CH or N; and n is 0-2; or

wherein in (9),

S/(9) and T/(9) is C, or S/(9) is C and T/(9) is N, or S/(9) is N andT/(9) is C;

R is hydrogen, amino, methyl, trifluoromethyl, or halo;

U is hydrogen, halo, amino, cyano, nitro, trifluoromethyl, (C₁-C₈)alkyl,(C₃-C₈)cycloalkyl, —COR^(a), —CO₂R^(a), —CONR^(a)R^(b), —SO₂R^(a),—SO₂NR^(a)R^(b), —NR^(a)R^(b), —NR^(a)C(O)R^(b),—NR^(a)SO₂R^(b),

—NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b), —NR^(a)NR^(a)C(O)R^(b),—OR^(a), or 4-(1H-pyrazol-4-yl),

-   -   wherein any (C₁-C₈)alkyl or (C₃-C₈)cycloalkyl group is        optionally substituted by 1, 2 or 3 groups independently        selected from (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl,        (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano, —COR^(a),        —CO₂R^(a),—CONR^(a)R^(b), —SR^(a), SOR^(a), —SO₂R^(a),        —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b),        —NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b),        —NR^(a)SO₂NR^(a)R^(b), —OR^(a),—OC(O)R^(a), and        —OC(O)NR^(a)R^(b); wherein R^(a) and R^(b) are defined as above.

Subgroup B of Formula (VII)

X and Z are selected independently from the group consisting of(C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, heteroaryl,—NR^(a)R^(b), and —OR^(a);

Y is H;

R¹ is (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, or heterocycloalkyl;

R² is hydrogen, (C₁-C₃)alkyl, or halo, in which said (C₁-C₃)alkyl isoptionally substituted with one to two groups selected from amino and(C₁-C₃)alkylamino;

R⁷ is hydrogen, (C₁-C₃)alkyl, or alkoxy;

R³ is hydrogen, (C₁-C₈)alkyl or halo;

R⁶ is hydrogen, halo, cyano, trifluoromethyl, amino, (C₁-C₈)alkyl,(C₃-C₈)cycloalkyl, aryl, heteroaryl, acylamino; (C₂-C₈)alkynyl,arylalkynyl, heteroarylalkynyl, —SO₂R^(a), —SO₂NR^(a)R^(b), or

—NR^(a)SO₂R^(b);

-   -   wherein any (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, (C₂-C₈)alkynyl,        arylalkynyl, or heteroarylalkynyl group is optionally        substituted by 1, 2 or 3 groups independently selected from        halo, (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl,        (C₁-C₆)haloalkyl, cyano, —COR^(a), —CO₂R^(a), —CONR^(a)R^(b),        —SR^(a), —SOR^(a), —SO₂R^(a),—SO₂NR^(a)R^(b), nitro,        —NR^(a)R^(b), —NR^(a)C(O)R^(b), —NR^(a)C(O)NR^(a)R^(b),        —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b),        —OR^(a), —OC(O)R^(a), —OC(O)NR^(a)R^(b), heterocycloalkyl, aryl,        heteroaryl, aryl(C₁-C₄)alkyl, and heteroaryl(C₁-C₄)alkyl;

R^(a) and R^(b) are each independently hydrogen, (C₁-C₈)alkyl,(C₂-C₈)alkenyl, (C₂-C₈)alkynyl, (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl,(C₆-C₁₀)bicycloalkyl, heterocycloalkyl, aryl, or heteroaryl, whereinsaid (C₁-C₈)alkyl, (C₂-C₈)alkenyl, (C₂-C₈)alkynyl, cycloalkyl,cycloalkenyl, bicycloalkyl, heterocycloalkyl, aryl or heteroaryl groupis optionally substituted by 1, 2 or 3 groups independently selectedfrom halo, hydroxyl, (C₁-C₄)alkoxy, amino, (C₁-C₄)alkylamino,((C₁-C₄)alkyl)((C₁-C₄)alkyl)amino, —CO₂H, —CO₂(C₁-C₄)alkyl,—CONH₂,—CONH(C₁-C₄)alkyl,

—CON((C₁-C₄)alkyl)((C₁-C₄)alkyl), —SO₂(C₁-C₄)alkyl, —SO₂NH₂,—SO₂NH(C₁-C₄)alkyl, and —SO₂N((C₁-C₄)alkyl)((C₁-C₄)alkyl);

or R^(a) and R^(b) taken together with the nitrogen to which they areattached represent a 5-8 membered saturated or unsaturated ring,optionally containing an additional heteroatom selected from oxygen,nitrogen, and sulfur, wherein said ring is optionally substituted by 1,2 or 3 groups independently selected from (C₁-C₄)alkyl,(C₁-C₄)haloalkyl, amino, (C₁-C₄)alkylamino,((C₁-C₄)alkyl)((C₁-C₄)alkyl)amino, hydroxyl, oxo, (C₁-C₄)alkoxy, and(C₁-C₄)alkoxy(C₁-C₄)alkyl, wherein said ring is optionally fused to a(C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring;

or R^(a) and R^(b) taken together with the nitrogen to which they areattached represent a 6- to 10-membered bridged bicyclic ring systemoptionally fused to a (C₃-C₈)cycloalkyl, heterocycloalkyl, aryl, orheteroaryl ring. Aryl and heteroaryl in this definition are selectedfrom the group consisting of furan, thiophene, pyrrole, oxazole,thiazole, imidazole, pyrazole, oxadiazole, thiadiazole, triazole,tetrazole, benzofuran, benzothiophene, benzoxazole, benzothiazole,phenyl, pyridine, pyridazine, pyrimidine, pyrazine, triazine, tetrazine,quinoline, cinnoline, quinazoline, quinoxaline, and naphthyridine or acompound of another aryl or heteroaryl group as follows:

wherein in (1),

A is O, NH, or S; B is CH or N, and C is hydrogen or C₁-C₈ alkyl; or

wherein in (2),

D is N or C optionally substituted by hydrogen or C₁-C₈ alkyl; or

wherein in (3),

E is NH or CH₂; F is O or CO; and G is NH or CH₂; or

wherein in (4),

J is O, S or CO; or

wherein in (5),

Q is CH or N;

M is CH or N; and

L/(5) is hydrogen, halo, amino, cyano, (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl,—COR^(a), —CO₂R^(a), —CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b), —SO₂R^(a),—SO₂NR^(a)R^(b), —NR^(a)R^(b), —NR^(a)C(O)R^(b),—NR^(a)SO₂R^(b),—NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b), —NR^(a)NR^(a)C(O)R^(b),—NR^(a)NR^(a)C(O)NR^(a)R^(b), or —OR^(a),

-   -   wherein any (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, group is optionally        substituted by 1, 2 or 3 groups independently selected from        (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl, (C₅-C₈)cycloalkenyl,        (C₁-C₆)haloalkyl, cyano, —COR^(a), —CO₂R^(a), —CONR^(a)R^(b),        —SR^(a), —SOR^(a), —SO₂R^(a), —SO₂NR^(a)R^(b), nitro,        —NR^(a)R^(b), —NR^(a)C(O)R^(b), —NR^(a)C(O)NR^(a)R^(b),        —NR^(a)C(O)OR^(a), NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b),        —OR^(a), —OC(O)R^(a), and —OC(O)NR^(a)R^(b),        wherein R^(a) and R^(b) are defined as above; or

wherein in (6),

L/(6) is NH or CH₂; or

wherein in (7),

-   -   M/(7) is hydrogen, halo, amino, cyano, (C₁-C₈)alkyl,        (C₃-C₈)cycloalkyl, heterocycloalkyl, —COR^(a),—CO₂R^(a),        —CONR^(a)R^(b), —CONR^(a)NR^(a)R^(b),—SO₂R^(a), —SO₂NR^(a)R^(b),        —NR^(a)R^(b), —NR^(a)C(O)R^(b),—NR^(a)SO₂R^(b),        —NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b),        —NR^(a)NR^(a)C(O)R^(b), —NR^(a)NR^(a)C(O)NR^(a)R^(b), or        —OR^(a),    -   wherein any (C₁-C₈)alkyl, (C₃-C₈)cycloalkyl, heterocycloalkyl        group is optionally substituted by 1, 2 or 3 groups        independently selected from (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl,        (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano, —COR^(a),        —CO₂R^(a), —CONR^(a)R^(b),—SR^(a), —SOR^(a), —SO₂R^(a),        —SO₂NR^(a)R^(b), nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b),        NR^(a)C(O)NR^(a)R^(b), —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b),        —NR^(a)SO₂NR^(a)R^(b), —OR^(a), —OC(O)R^(a), —OC(O)NR^(a)R^(b);        wherein R^(a) and R^(b) are defined as above; or

wherein in (8),

P is CH₂, NH, O, or S; Q/(8) is CH or N; and n is 0-2; or

wherein in (9),

S/(9) and T/(9) is C, or S/(9) is C and T/(9) is N, or S/(9) is N andT/(9) is C;

R is hydrogen, amino, methyl, trifluoromethyl, halo;

U is hydrogen, halo, amino, cyano, nitro, trifluoromethyl, (C₁-C₈)alkyl,(C₃-C₈)cycloalkyl, —COR^(a), —CO₂R^(a), —CONR^(a)R^(b), —SO₂R^(a),—SO₂NR^(a)R^(b), —NR^(a)R^(b), —NR^(a)C(O)R^(b),—NR^(a)SO₂R^(b),

—NR^(a)SO₂NR^(a)R^(b), —NR^(a)NR^(a)R^(b), —NR^(a)NR^(a)C(O)R^(b),—OR^(a), or 4-(1H-pyrazol-4-yl),

-   -   wherein any (C₁-C₈)alkyl, or (C₃-C₈)cycloalkyl group is        optionally substituted by 1, 2 or 3 groups independently        selected from (C₁-C₆)alkyl, (C₃-C₈)cycloalkyl,        (C₅-C₈)cycloalkenyl, (C₁-C₆)haloalkyl, cyano, —COR^(a),        —CO₂R^(a),—CONR^(a)R^(b),—SOR^(a),—SO₂R^(a), —SO₂NR^(a)R^(b),        nitro, —NR^(a)R^(b), —NR^(a)C(O)R^(b), —NR^(a)C(O)NR^(a)R^(b),        —NR^(a)C(O)OR^(a), —NR^(a)SO₂R^(b), —NR^(a)SO₂NR^(a)R^(b),        —OR^(a), —OC(O)R^(a), and —OC(O)NR^(a)R^(b), wherein R^(a) and        R^(b) are defined as above.

In some embodiments, the EZH2 inhibitor is:

stereoisomers thereof or pharmaceutically acceptable salt or solvatethereof.

In some embodiments, the EZH2 inhibitor is

stereoisomers thereof or pharmaceutically acceptable salt or solvatethereof.

The compounds described herein can be synthesized according to anymethod known in the art. For example, the compounds having the Formula(VII) can be synthesized according to the method described in WO2011/140325; WO 2011/140324; and WO 2012/005805, each of which isincorporated by reference in its entirety.

As used herein, “alkyl”, “C₁, C₂, C₃, C₄, C₅ or C₆ alkyl” or “C₁-C₆alkyl” is intended to include C₁, C₂, C₃, C₄, C₅ or C₆ straight chain(linear) saturated aliphatic hydrocarbon groups and C₃, C₄, C₅ or C₆branched saturated aliphatic hydrocarbon groups. For example, C₁-C₆alkyl is intended to include C₁, C₂, C₃, C₄, C₅ and C₆ alkyl groups.Examples of alkyl include, moieties having from one to six carbon atoms,such as, but not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl,s-butyl, t-butyl, n-pentyl, s-pentyl or n-hexyl.

In certain embodiments, a straight chain or branched alkyl has six orfewer carbon atoms (e.g., C₁-C₆ for straight chain, C₃-C₆ for branchedchain), and in another embodiment, a straight chain or branched alkylhas four or fewer carbon atoms.

As used herein, the term “cycloalkyl” refers to a saturated orunsaturated nonaromatic hydrocarbon mono- or multi-ring (e.g., fused,bridged, or spiro rings) system having 3 to 30 carbon atoms (e.g.,C₃-C₁₀). Examples of cycloalkyl include, but are not limited to,cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl,cyclooctyl, cyclopentenyl, cyclohexenyl, cycloheptenyl, and adamantyl.The term “heterocycloalkyl” refers to a saturated or unsaturatednonaromatic 3-8 membered monocyclic, 7-12 membered bicyclic (fused,bridged, or spiro rings), or 11-14 membered tricyclic ring system(fused, bridged, or spiro rings) having one or more heteroatoms (such asO, N, S, or Se), unless specified otherwise. Examples ofheterocycloalkyl groups include, but are not limited to, piperidinyl,piperazinyl, pyrrolidinyl, dioxanyl, tetrahydrofuranyl, isoindolinyl,indolinyl, imidazolidinyl, pyrazolidinyl, oxazolidinyl, isoxazolidinyl,triazolidinyl, tetrahyrofuranyl, oxiranyl, azetidinyl, oxetanyl,thietanyl, 1,2,3,6-tetrahydropyridinyl, tetrahydropyranyl,dihydropyranyl, pyranyl, morpholinyl, 1,4-diazepanyl, 1,4-oxazepanyl,2-oxa-5-azabicyclo[2.2.1]heptanyl, diazabicyclo[2.2.1]heptanyl,2-oxa-6-azaspiro[3.3]heptanyl, 2,6-diazaspiro[3.3]heptanyl,1,4-dioxa-8-azaspiro[4.5]decanyl and the like.

The term “optionally substituted alkyl” refers to unsubstituted alkyl oralkyl having designated substituents replacing one or more hydrogenatoms on one or more carbons of the hydrocarbon backbone. Suchsubstituents can include, for example, alkyl, alkenyl, alkynyl, halogen,hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl,alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl,alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino(including alkylamino, dialkylamino, arylamino, diarylamino andalkylarylamino), acylamino (including alkylcarbonylamino,arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl,alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl,sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido,heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

An “arylalkyl” or an “aralkyl” moiety isan alkyl substituted with anaryl (e.g., phenylmethyl (benzyl)). An “alkylaryl” moiety isan arylsubstituted with an alkyl (e.g., methylphenyl).

As used herein, “alkyl linker” is intended to include C₁, C₂, C₃, C₄, C₅or C₆ straight chain (linear) saturated divalent aliphatic hydrocarbongroups and C₃, C₄, C₅ or C₆ branched saturated aliphatic hydrocarbongroups. For example, C₁-C₆ alkyl linker is intended to include C₁, C₂,C₃, C₄, C₅ and C₆ alkyl linker groups. Examples of alkyl linker include,moieties having from one to six carbon atoms, such as, but not limitedto, methyl (—CH₂—), ethyl (—CH₂CH₂—), n-propyl (—CH₂CH₂CH₂—), i-propyl(—CHCH₃CH₂—), n-butyl (—CH₂CH₂CH₂CH₂—), s-butyl (—CHCH₃CH₂CH₂—), i-butyl(—C(CH₃)₂CH₂—), n-pentyl (—CH₂CH₂CH₂CH₂CH₂—), s-pentyl(—CHCH₃CH₂CH₂CH₂—) or n-hexyl (—CH₂CH₂CH₂CH₂CH₂CH₂—).

“Alkenyl” includes unsaturated aliphatic groups analogous in length andpossible substitution to the alkyls described above, but that contain atleast one double bond. For example, the term “alkenyl” includes straightchain alkenyl groups (e.g., ethenyl, propenyl, butenyl, pentenyl,hexenyl, heptenyl, octenyl, nonenyl, decenyl), and branched alkenylgroups. In certain embodiments, a straight chain or branched alkenylgroup has six or fewer carbon atoms in its backbone (e.g., C₂-C₆ forstraight chain, C₃-C₆ for branched chain). The term “C₂-C₆” includesalkenyl groups containing two to six carbon atoms. The term “C₃-C₆”includes alkenyl groups containing three to six carbon atoms.

The term “optionally substituted alkenyl” refers to unsubstitutedalkenyl or alkenyl having designated substituents replacing one or morehydrogen atoms on one or more hydrocarbon backbone carbon atoms. Suchsubstituents can include, for example, alkyl, alkenyl, alkynyl, halogen,hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl,alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl,alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino(including alkylamino, dialkylamino, arylamino, diarylamino andalkylarylamino), acylamino (including alkylcarbonylamino,arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl,alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl,sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano,heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

“Alkynyl” includes unsaturated aliphatic groups analogous in length andpossible substitution to the alkyls described above, but which containat least one triple bond. For example, “alkynyl” includes straight chainalkynyl groups (e.g., ethynyl, propynyl, butynyl, pentynyl, hexynyl,heptynyl, octynyl, nonynyl, decynyl), and branched alkynyl groups. Incertain embodiments, a straight chain or branched alkynyl group has sixor fewer carbon atoms in its backbone (e.g., C₂-C₆ for straight chain,C₃-C₆ for branched chain). The term “C₂-C₆” includes alkynyl groupscontaining two to six carbon atoms. The term “C₃-C₆” includes alkynylgroups containing three to six carbon atoms.

The term “optionally substituted alkynyl” refers to unsubstitutedalkynyl or alkynyl having designated substituents replacing one or morehydrogen atoms on one or more hydrocarbon backbone carbon atoms. Suchsubstituents can include, for example, alkyl, alkenyl, alkynyl, halogen,hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, arylcarbonyl,alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl, dialkylaminocarbonyl,alkylthiocarbonyl, alkoxyl, phosphate, phosphonato, phosphinato, amino(including alkylamino, dialkylamino, arylamino, diarylamino andalkylarylamino), acylamino (including alkylcarbonylamino,arylcarbonylamino, carbamoyl and ureido), amidino, imino, sulfhydryl,alkylthio, arylthio, thiocarboxylate, sulfates, alkylsulfinyl,sulfonato, sulfamoyl, sulfonamido, nitro, trifluoromethyl, cyano, azido,heterocyclyl, alkylaryl, or an aromatic or heteroaromatic moiety.

Other optionally substituted moieties (such as optionally substitutedcycloalkyl, heterocycloalkyl, aryl, or heteroaryl) include both theunsubstituted moieties and the moieties having one or more of thedesignated substituents. For example, substituted heterocycloalkylincludes those substituted with one or more alkyl groups, such as2,2,6,6-tetramethyl-piperidinyl and2,2,6,6-tetramethyl-1,2,3,6-tetrahydropyridinyl.

“Aryl” includes groups with aromaticity, including “conjugated,” ormulticyclic systems with at least one aromatic ring and do not containany heteroatom in the ring structure. Examples include phenyl, benzyl,1,2,3,4-tetrahydronaphthalenyl, etc.

“Heteroaryl” groups are aryl groups, as defined above, except havingfrom one to four heteroatoms in the ring structure, and may also bereferred to as “aryl heterocycles” or “heteroaromatics.” As used herein,the term “heteroaryl” is intended to include a stable 5-, 6-, or7-membered monocyclic or 7-, 8-, 9-, 10-, 11- or 12-membered bicyclicaromatic heterocyclic ring which consists of carbon atoms and one ormore heteroatoms, e.g., 1 or 1-2 or 1-3 or 1-4 or 1-5 or 1-6heteroatoms, or e.g. 2, 3, 4, 5, or 6 heteroatoms, independentlyselected from the group consisting of nitrogen, oxygen and sulfur. Thenitrogen atom may be substituted or unsubstituted (i.e., N or NR whereinR is H or other substituents, as defined). The nitrogen and sulfurheteroatoms may optionally be oxidized (i.e., N→O and S(O)_(p), wherep=1 or 2). It is to be noted that total number of S and O atoms in thearomatic heterocycle is not more than 1.

Examples of heteroaryl groups include pyrrole, furan, thiophene,thiazole, isothiazole, imidazole, triazole, tetrazole, pyrazole,oxazole, isoxazole, pyridine, pyrazine, pyridazine, pyrimidine, and thelike.

Furthermore, the terms “aryl” and “heteroaryl” include multicyclic aryland heteroaryl groups, e.g., tricyclic, bicyclic, e.g., naphthalene,benzoxazole, benzodioxazole, benzothiazole, benzoimidazole,benzothiophene, methylenedioxyphenyl, quinoline, isoquinoline,naphthrydine, indole, benzofuran, purine, benzofuran, deazapurine,indolizine.

In the case of multicyclic aromatic rings, only one of the rings needsto be aromatic (e.g., 2,3-dihydroindole), although all of the rings maybe aromatic (e.g., quinoline). The second ring can also be fused orbridged.

The cycloalkyl, heterocycloalkyl, aryl, or heteroaryl ring can besubstituted at one or more ring positions (e.g., the ring-forming carbonor heteroatom such as N) with such substituents as described above, forexample, alkyl, alkenyl, alkynyl, halogen, hydroxyl, alkoxy,alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, alkylcarbonyl, alkylaminocarbonyl,aralkylaminocarbonyl, alkenylaminocarbonyl, alkylcarbonyl, arylcarbonyl,aralkylcarbonyl, alkenylcarbonyl, alkoxycarbonyl, aminocarbonyl,alkylthiocarbonyl, phosphate, phosphonato, phosphinato, amino (includingalkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino),acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyland ureido), amidino, imino, sulfhydryl, alkylthio, arylthio,thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl,sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl,alkylaryl, or an aromatic or heteroaromatic moiety. Aryl and heteroarylgroups can also be fused or bridged with alicyclic or heterocyclicrings, which are not aromatic so as to form a multicyclic system (e.g.,tetralin, methylenedioxyphenyl).

As used herein, “carbocycle” or “carbocyclic ring” is intended toinclude any stable monocyclic, bicyclic or tricyclic ring having thespecified number of carbons, any of which may be saturated, unsaturated,or aromatic. Carbocycle includes cycloalkyl and aryl. For example, aC₃-C₁₄ carbocycle is intended to include a monocyclic, bicyclic ortricyclic ring having 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 or 14 carbonatoms. Examples of carbocycles include, but are not limited to,cyclopropyl, cyclobutyl, cyclobutenyl, cyclopentyl, cyclopentenyl,cyclohexyl, cycloheptenyl, cycloheptyl, cycloheptenyl, adamantyl,cyclooctyl, cyclooctenyl, cyclooctadienyl, fluorenyl, phenyl, naphthyl,indanyl, adamantyl and tetrahydronaphthyl. Bridged rings are alsoincluded in the definition of carbocycle, including, for example,[3.3.0]bicyclooctane, [4.3.0]bicyclononane, [4.4.0]bicyclodecane and[2.2.2]bicyclooctane. A bridged ring occurs when one or more carbonatoms link two non-adjacent carbon atoms. In one embodiment, bridgerings are one or two carbon atoms. It is noted that a bridge alwaysconverts a monocyclic ring into a tricyclic ring. When a ring isbridged, the substituents recited for the ring may also be present onthe bridge. Fused (e.g., naphthyl, tetrahydronaphthyl) and spiro ringsare also included.

As used herein, “heterocycle” or “heterocyclic group” includes any ringstructure (saturated, unsaturated, or aromatic) which contains at leastone ring heteroatom (e.g., N, O or S). Heterocycle includesheterocycloalkyl and heteroaryl. Examples of heterocycles include, butare not limited to, morpholine, pyrrolidine, tetrahydrothiophene,piperidine, piperazine, oxetane, pyran, tetrahydropyran, azetidine, andtetrahydrofuran.

Examples of heterocyclic groups include, but are not limited to,acridinyl, azocinyl, benzimidazolyl, benzofuranyl, benzothiofuranyl,benzothiophenyl, benzoxazolyl, benzoxazolinyl, benzthiazolyl,benztriazolyl, benztetrazolyl, benzisoxazolyl, benzisothiazolyl,benzimidazolinyl, carbazolyl, 4aH-carbazolyl, carbolinyl, chromanyl,chromenyl, cinnolinyl, decahydroquinolinyl, 2H,6H-1,5,2-dithiazinyl,dihydrofuro[2,3-b]tetrahydrofuran, furanyl, furazanyl, imidazolidinyl,imidazolinyl, imidazolyl, 1H-indazolyl, indolenyl, indolinyl,indolizinyl, indolyl, 3H-indolyl, isatinoyl, isobenzofuranyl,isochromanyl, isoindazolyl, isoindolinyl, isoindolyl, isoquinolinyl,isothiazolyl, isoxazolyl, methylenedioxyphenyl, morpholinyl,naphthyridinyl, octahydroisoquinolinyl, oxadiazolyl, 1,2,3-oxadiazolyl,1,2,4-oxadiazolyl, 1,2,5-oxadiazolyl, 1,3,4-oxadiazolyl,1,2,4-oxadiazol5(4H)-one, oxazolidinyl, oxazolyl, oxindolyl,pyrimidinyl, phenanthridinyl, phenanthrolinyl, phenazinyl,phenothiazinyl, phenoxathinyl, phenoxazinyl, phthalazinyl, piperazinyl,piperidinyl, piperidonyl, 4-piperidonyl, piperonyl, pteridinyl, purinyl,pyranyl, pyrazinyl, pyrazolidinyl, pyrazolinyl, pyrazolyl, pyridazinyl,pyridooxazole, pyridoimidazole, pyridothiazole, pyridinyl, pyridyl,pyrimidinyl, pyrrolidinyl, pyrrolinyl, 2H-pyrrolyl, pyrrolyl,quinazolinyl, quinolinyl, 4H-quinolizinyl, quinoxalinyl, quinuclidinyl,tetrahydrofuranyl, tetrahydroisoquinolinyl, tetrahydroquinolinyl,tetrazolyl, 6H-1,2,5-thiadiazinyl, 1,2,3-thiadiazolyl,1,2,4-thiadiazolyl, 1,2,5-thiadiazolyl, 1,3,4-thiadiazolyl,thianthrenyl, thiazolyl, thienyl, thienothiazolyl, thienooxazolyl,thienoimidazolyl, thiophenyl, triazinyl, 1,2,3-triazolyl,1,2,4-triazolyl, 1,2,5-triazolyl, 1,3,4-triazolyl and xanthenyl.

The term “substituted,” as used herein, means that any one or morehydrogen atoms on the designated atom is replaced with a selection fromthe indicated groups, provided that the designated atom's normal valencyis not exceeded, and that the substitution results in a stable compound.When a substituent is oxo or keto (i.e., ═O), then 2 hydrogen atoms onthe atom are replaced. Keto substituents are not present on aromaticmoieties. Ring double bonds, as used herein, are double bonds that areformed between two adjacent ring atoms (e.g., C═C, C═N or N═N). “Stablecompound” and “stable structure” are meant to indicate a compound thatis sufficiently robust to survive isolation to a useful degree of purityfrom a reaction mixture, and formulation into an efficacious therapeuticagent.

When a bond to a substituent is shown to cross a bond connecting twoatoms in a ring, then such substituent may be bonded to any atom in thering. When a substituent is listed without indicating the atom via whichsuch substituent is bonded to the rest of the compound of a givenformula, then such substituent may be bonded via any atom in suchformula. Combinations of substituents and/or variables are permissible,but only if such combinations result in stable compounds.

When any variable (e.g., R₁) occurs more than one time in anyconstituent or formula for a compound, its definition at each occurrenceis independent of its definition at every other occurrence. Thus, forexample, if a group is shown to be substituted with 0-2 R₁ moieties,then the group may optionally be substituted with up to two R₁ moietiesand R₁ at each occurrence is selected independently from the definitionof R₁. Also, combinations of substituents and/or variables arepermissible, but only if such combinations result in stable compounds.

The term “hydroxy” or “hydroxyl” includes groups with an —OH or —O⁻.

As used herein, “halo” or “halogen” refers to fluoro, chloro, bromo andiodo. The term “perhalogenated” generally refers to a moiety wherein allhydrogen atoms are replaced by halogen atoms. The term “haloalkyl” or“haloalkoxyl” refers to an alkyl or alkoxyl substituted with one or morehalogen atoms.

The term “carbonyl” includes compounds and moieties which contain acarbon connected with a double bond to an oxygen atom. Examples ofmoieties containing a carbonyl include, but are not limited to,aldehydes, ketones, carboxylic acids, amides, esters, anhydrides, etc.

The term “carboxyl” refers to —COOH or its C₁-C₆ alkyl ester.

“Acyl” includes moieties that contain the acyl radical (R—C(O)—) or acarbonyl group. “Substituted acyl” includes acyl groups where one ormore of the hydrogen atoms are replaced by, for example, alkyl groups,alkynyl groups, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy,alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl,arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl,dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate,phosphonato, phosphinato, amino (including alkylamino, dialkylamino,arylamino, diarylamino and alkylarylamino), acylamino (includingalkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino,imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates,alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro,trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromaticor heteroaromatic moiety.

“Aroyl” includes moieties with an aryl or heteroaromatic moiety bound toa carbonyl group. Examples of aroyl groups include phenylcarboxy,naphthyl carboxy, etc.

“Alkoxyalkyl,” “alkylaminoalkyl,” and “thioalkoxyalkyl” include alkylgroups, as described above, wherein oxygen, nitrogen, or sulfur atomsreplace one or more hydrocarbon backbone carbon atoms.

The term “alkoxy” or “alkoxyl” includes substituted and unsubstitutedalkyl, alkenyl and alkynyl groups covalently linked to an oxygen atom.Examples of alkoxy groups or alkoxyl radicals include, but are notlimited to, methoxy, ethoxy, isopropyloxy, propoxy, butoxy and pentoxygroups. Examples of substituted alkoxy groups include halogenated alkoxygroups. The alkoxy groups can be substituted with groups such asalkenyl, alkynyl, halogen, hydroxyl, alkylcarbonyloxy, arylcarbonyloxy,alkoxycarbonyloxy, aryloxycarbonyloxy, carboxylate, alkylcarbonyl,arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl,dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, phosphate,phosphonato, phosphinato, amino (including alkylamino, dialkylamino,arylamino, diarylamino, and alkylarylamino), acylamino (includingalkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido), amidino,imino, sulfhydryl, alkylthio, arylthio, thiocarboxylate, sulfates,alkylsulfinyl, sulfonato, sulfamoyl, sulfonamido, nitro,trifluoromethyl, cyano, azido, heterocyclyl, alkylaryl, or an aromaticor heteroaromatic moieties. Examples of halogen substituted alkoxygroups include, but are not limited to, fluoromethoxy, difluoromethoxy,trifluoromethoxy, chloromethoxy, dichloromethoxy and trichloromethoxy.

The term “ether” or “alkoxy” includes compounds or moieties whichcontain an oxygen bonded to two carbon atoms or heteroatoms. Forexample, the term includes “alkoxyalkyl,” which refers to an alkyl,alkenyl, or alkynyl group covalently bonded to an oxygen atom which iscovalently bonded to an alkyl group.

The term “ester” includes compounds or moieties which contain a carbonor a heteroatom bound to an oxygen atom which is bonded to the carbon ofa carbonyl group. The term “ester” includes alkoxycarboxy groups such asmethoxycarbonyl, ethoxycarbonyl, propoxycarbonyl, butoxycarbonyl,pentoxycarbonyl, etc.

The term “thioalkyl” includes compounds or moieties which contain analkyl group connected with a sulfur atom. The thioalkyl groups can besubstituted with groups such as alkyl, alkenyl, alkynyl, halogen,hydroxyl, alkylcarbonyloxy, arylcarbonyloxy, alkoxycarbonyloxy,aryloxycarbonyloxy, carboxylate, carboxyacid, alkylcarbonyl,arylcarbonyl, alkoxycarbonyl, aminocarbonyl, alkylaminocarbonyl,dialkylaminocarbonyl, alkylthiocarbonyl, alkoxyl, amino (includingalkylamino, dialkylamino, arylamino, diarylamino and alkylarylamino),acylamino (including alkylcarbonylamino, arylcarbonylamino, carbamoyland ureido), amidino, imino, sulfhydryl, alkylthio, arylthio,thiocarboxylate, sulfates, alkylsulfinyl, sulfonato, sulfamoyl,sulfonamido, nitro, trifluoromethyl, cyano, azido, heterocyclyl,alkylaryl, or an aromatic or heteroaromatic moieties.

The term “thiocarbonyl” or “thiocarboxy” includes compounds and moietieswhich contain a carbon connected with a double bond to a sulfur atom.

The term “thioether” includes moieties which contain a sulfur atombonded to two carbon atoms or heteroatoms. Examples of thioethersinclude, but are not limited to alkthioalkyls, alkthioalkenyls, andalkthioalkynyls. The term “alkthioalkyls” include moieties with analkyl, alkenyl, or alkynyl group bonded to a sulfur atom which is bondedto an alkyl group. Similarly, the term “alkthioalkenyls” refers tomoieties wherein an alkyl, alkenyl or alkynyl group is bonded to asulfur atom which is covalently bonded to an alkenyl group; andalkthioalkynyls” refers to moieties wherein an alkyl, alkenyl or alkynylgroup is bonded to a sulfur atom which is covalently bonded to analkynyl group.

As used herein, “amine” or “amino” refers to unsubstituted orsubstituted —NH₂. “Alkylamino” includes groups of compounds whereinnitrogen of —NH₂ is bound to at least one alkyl group. Examples ofalkylamino groups include benzylamino, methylamino, ethylamino,phenethylamino, etc. “Dialkylamino” includes groups wherein the nitrogenof —NH₂ is bound to at least two additional alkyl groups. Examples ofdialkylamino groups include, but are not limited to, dimethylamino anddiethylamino. “Arylamino” and “diarylamino” include groups wherein thenitrogen is bound to at least one or two aryl groups, respectively.“Aminoaryl” and “aminoaryloxy” refer to aryl and aryloxy substitutedwith amino. “Alkylarylamino,” “alkylaminoaryl” or “arylaminoalkyl”refers to an amino group which is bound to at least one alkyl group andat least one aryl group. “Alkaminoalkyl” refers to an alkyl, alkenyl, oralkynyl group bound to a nitrogen atom which is also bound to an alkylgroup. “Acylamino” includes groups wherein nitrogen is bound to an acylgroup. Examples of acylamino include, but are not limited to,alkylcarbonylamino, arylcarbonylamino, carbamoyl and ureido groups.

The term “amide” or “aminocarboxy” includes compounds or moieties thatcontain a nitrogen atom that is bound to the carbon of a carbonyl or athiocarbonyl group. The term includes “alkaminocarboxy” groups thatinclude alkyl, alkenyl or alkynyl groups bound to an amino group whichis bound to the carbon of a carbonyl or thiocarbonyl group. It alsoincludes “arylaminocarboxy” groups that include aryl or heteroarylmoieties bound to an amino group that is bound to the carbon of acarbonyl or thiocarbonyl group. The terms “alkylaminocarboxy”,“alkenylaminocarboxy”, “alkynylaminocarboxy” and “arylaminocarboxy”include moieties wherein alkyl, alkenyl, alkynyl and aryl moieties,respectively, are bound to a nitrogen atom which is in turn bound to thecarbon of a carbonyl group. Amides can be substituted with substituentssuch as straight chain alkyl, branched alkyl, cycloalkyl, aryl,heteroaryl or heterocycle. Substituents on amide groups may be furthersubstituted.

In the present specification, the structural formula of the compoundrepresents a certain isomer for convenience in some cases, but thepresent invention includes all isomers, such as geometrical isomers,optical isomers based on an asymmetrical carbon, stereoisomers,tautomers, and the like, it being understood that not all isomers mayhave the same level of activity. In addition, a crystal polymorphism maybe present for the compounds represented by the formula. It is notedthat any crystal form, crystal form mixture, or anhydride or hydratethereof is included in the scope of the present invention. Furthermore,so-called metabolite which is produced by degradation of the presentcompound in vivo is included in the scope of the present invention.

“Isomerism” means compounds that have identical molecular formulae butdiffer in the sequence of bonding of their atoms or in the arrangementof their atoms in space. Isomers that differ in the arrangement of theiratoms in space are termed “stereoisomers.” Stereoisomers that are notmirror images of one another are termed “diastereoisomers,” andstereoisomers that are non-superimposable mirror images of each otherare termed “enantiomers” or sometimes optical isomers. A mixturecontaining equal amounts of individual enantiomeric forms of oppositechirality is termed a “racemic mixture.”

A carbon atom bonded to four nonidentical substituents is termed a“chiral center.”

“Chiral isomer” means a compound with at least one chiral center.Compounds with more than one chiral center may exist either as anindividual diastereomer or as a mixture of diastereomers, termed“diastereomeric mixture.” When one chiral center is present, astereoisomer may be characterized by the absolute configuration (R or S)of that chiral center. Absolute configuration refers to the arrangementin space of the substituents attached to the chiral center. Thesubstituents attached to the chiral center under consideration areranked in accordance with the Sequence Rule of Cahn, Ingold and Prelog.(Cahn et al., Angew. Chem. Inter. Edit. 1966, 5, 385; errata 511; Cahnet al., Angew. Chem. 1966, 78, 413; Cahn and Ingold, J. Chem. Soc. 1951(London), 612; Cahn et al., Experientia 1956, 12, 81; Cahn, J. Chem.Educ. 1964, 41, 116).

“Geometric isomer” means the diastereomers that owe their existence tohindered rotation about double bonds or a cycloalkyl linker (e.g.,1,3-cylcobutyl). These configurations are differentiated in their namesby the prefixes cis and trans, or Z and E, which indicate that thegroups are on the same or opposite side of the double bond in themolecule according to the Cahn-Ingold-Prelog rules.

It is to be understood that the compounds of the present invention maybe depicted as different chiral isomers or geometric isomers. It shouldalso be understood that when compounds have chiral isomeric or geometricisomeric forms, all isomeric forms are intended to be included in thescope of the present invention, and the naming of the compounds does notexclude any isomeric forms, it being understood that not all isomers mayhave the same level of activity.

Furthermore, the structures and other compounds discussed in thisinvention include all atropic isomers thereof, it being understood thatnot all atropic isomers may have the same level of activity. “Atropicisomers” are a type of stereoisomer in which the atoms of two isomersare arranged differently in space. Atropic isomers owe their existenceto a restricted rotation caused by hindrance of rotation of large groupsabout a central bond. Such atropic isomers typically exist as a mixture,however as a result of recent advances in chromatography techniques, ithas been possible to separate mixtures of two atropic isomers in selectcases.

“Tautomer” is one of two or more structural isomers that exist inequilibrium and is readily converted from one isomeric form to another.This conversion results in the formal migration of a hydrogen atomaccompanied by a switch of adjacent conjugated double bonds. Tautomersexist as a mixture of a tautomeric set in solution. In solutions wheretautomerization is possible, a chemical equilibrium of the tautomerswill be reached. The exact ratio of the tautomers depends on severalfactors, including temperature, solvent and pH. The concept of tautomersthat are interconvertable by tautomerizations is called tautomerism.

Of the various types of tautomerism that are possible, two are commonlyobserved. In keto-enol tautomerism a simultaneous shift of electrons anda hydrogen atom occurs. Ring-chain tautomerism arises as a result of thealdehyde group (—CHO) in a sugar chain molecule reacting with one of thehydroxy groups (—OH) in the same molecule to give it a cyclic(ring-shaped) form as exhibited by glucose.

Common tautomeric pairs are: ketone-enol, amide-nitrile, lactam-lactim,amide-imidic acid tautomerism in heterocyclic rings (e.g., innucleobases such as guanine, thymine and cytosine), imine-enamine andenamine-enamine. An example of keto-enol equilibria is betweenpyridin-2(1H)-ones and the corresponding pyridin-2-ols, as shown below.

It is to be understood that the compounds of the present invention maybe depicted as different tautomers. It should also be understood thatwhen compounds have tautomeric forms, all tautomeric forms are intendedto be included in the scope of the present invention, and the naming ofthe compounds does not exclude any tautomer form. It will be understoodthat certain tautomers may have a higher level of activity than others.

The term “crystal polymorphs”, “polymorphs” or “crystal forms” meanscrystal structures in which a compound (or a salt or solvate thereof)can crystallize in different crystal packing arrangements, all of whichhave the same elemental composition. Different crystal forms usuallyhave different X-ray diffraction patterns, infrared spectral, meltingpoints, density hardness, crystal shape, optical and electricalproperties, stability and solubility. Recrystallization solvent, rate ofcrystallization, storage temperature, and other factors may cause onecrystal form to dominate. Crystal polymorphs of the compounds can beprepared by crystallization under different conditions.

The compounds of any of Formulae disclosed herein include the compoundsthemselves, as well as their salts or their solvates, if applicable. Asalt, for example, can be formed between an anion and a positivelycharged group (e.g., amino) on an aryl- or heteroaryl-substitutedbenzene compound. Suitable anions include chloride, bromide, iodide,sulfate, bisulfate, sulfamate, nitrate, phosphate, citrate,methanesulfonate, trifluoroacetate, glutamate, glucuronate, glutarate,malate, maleate, succinate, fumarate, tartrate, tosylate, salicylate,lactate, naphthalenesulfonate, and acetate (e.g., trifluoroacetate). Theterm “pharmaceutically acceptable anion” refers to an anion suitable forforming a pharmaceutically acceptable salt. Likewise, a salt can also beformed between a cation and a negatively charged group (e.g.,carboxylate) on an aryl- or heteroaryl-substituted benzene compound.Suitable cations include sodium ion, potassium ion, magnesium ion,calcium ion, and an ammonium cation such as tetramethylammonium ion. Thearyl- or heteroaryl-substituted benzene compounds also include thosesalts containing quaternary nitrogen atoms.

Additionally, the compounds of the present invention, for example, thesalts of the compounds, can exist in either hydrated or unhydrated (theanhydrous) form or as solvates with other solvent molecules. Nonlimitingexamples of hydrates include monohydrates, dihydrates, etc. Nonlimitingexamples of solvates include ethanol solvates, acetone solvates, etc.

“Solvate” means solvent addition forms that contain eitherstoichiometric or non stoichiometric amounts of solvent. Some compoundshave a tendency to trap a fixed molar ratio of solvent molecules in thecrystalline solid state, thus forming a solvate. If the solvent is waterthe solvate formed is a hydrate; and if the solvent is alcohol, thesolvate formed is an alcoholate. Hydrates are formed by the combinationof one or more molecules of water with one molecule of the substance inwhich the water retains its molecular state as H₂O.

As used herein, the term “analog” refers to a chemical compound that isstructurally similar to another but differs slightly in composition (asin the replacement of one atom by an atom of a different element or inthe presence of a particular functional group, or the replacement of onefunctional group by another functional group). Thus, an analog is acompound that is similar or comparable in function and appearance, butnot in structure or origin to the reference compound.

As defined herein, the term “derivative” refers to compounds that have acommon core structure, and are substituted with various groups asdescribed herein. For example, all of the compounds represented byFormula (I) are aryl- or heteroaryl-substituted benzene compounds, andhave Formula (I) as a common core.

The term “bioisostere” refers to a compound resulting from the exchangeof an atom or of a group of atoms with another, broadly similar, atom orgroup of atoms. The objective of a bioisosteric replacement is to createa new compound with similar biological properties to the parentcompound. The bioisosteric replacement may be physicochemically ortopologically based. Examples of carboxylic acid bioisosteres include,but are not limited to, acyl sulfonimides, tetrazoles, sulfonates andphosphonates. See, e.g., Patani and LaVoie, Chem. Rev. 96, 3147-3176,1996.

The present invention is intended to include all isotopes of atomsoccurring in the present compounds. Isotopes include those atoms havingthe same atomic number but different mass numbers. By way of generalexample and without limitation, isotopes of hydrogen include tritium anddeuterium, and isotopes of carbon include C-13 and C-14.

The present invention provides methods for the synthesis of thecompounds of any Formula disclosed herein. The present invention alsoprovides detailed methods for the synthesis of various disclosedcompounds of the present invention according to the following schemes asshown in the Examples.

Throughout the description, where compositions are described as having,including, or comprising specific components, it is contemplated thatcompositions also consist essentially of, or consist of, the recitedcomponents. Similarly, where methods or processes are described ashaving, including, or comprising specific process steps, the processesalso consist essentially of, or consist of, the recited processingsteps. Further, it should be understood that the order of steps or orderfor performing certain actions is immaterial so long as the inventionremains operable. Moreover, two or more steps or actions can beconducted simultaneously.

The synthetic processes of the invention can tolerate a wide variety offunctional groups, therefore various substituted starting materials canbe used. The processes generally provide the desired final compound ator near the end of the overall process, although it may be desirable incertain instances to further convert the compound to a pharmaceuticallyacceptable salt, polymorph or solvate thereof.

Compounds of the present invention can be prepared in a variety of waysusing commercially available starting materials, compounds known in theliterature, or from readily prepared intermediates, by employingstandard synthetic methods and procedures either known to those skilledin the art, or which will be apparent to the skilled artisan in light ofthe teachings herein. Standard synthetic methods and procedures for thepreparation of organic molecules and functional group transformationsand manipulations can be obtained from the relevant scientificliterature or from standard textbooks in the field. Although not limitedto any one or several sources, classic texts such as Smith, M. B.,March, J., March's Advanced Organic Chemistry: Reactions, Mechanisms,and Structure, 5^(th) edition, John Wiley & Sons: New York, 2001;Greene, T. W., Wuts, P. G. M., Protective Groups in Organic Synthesis,3^(rd) edition, John Wiley & Sons: New York, 1999; R. Larock,Comprehensive Organic Transformations, VCH Publishers (1989); L. Fieserand M. Fieser, Fieser and Fieser's Reagents for Organic Synthesis, JohnWiley and Sons (1994); and L. Paquette, ed., Encyclopedia of Reagentsfor Organic Synthesis, John Wiley and Sons (1995), incorporated byreference herein, are useful and recognized reference textbooks oforganic synthesis known to those in the art. The following descriptionsof synthetic methods are designed to illustrate, but not to limit,general procedures for the preparation of compounds of the presentinvention.

Compounds of the present invention can be conveniently prepared by avariety of methods familiar to those skilled in the art. The compoundsof this invention with any Formula disclosed herein may be preparedaccording to the procedures illustrated in Schemes 1-10 below, fromcommercially available starting materials or starting materials whichcan be prepared using literature procedures. The Z and R groups (such asR₂, R₃, R₄, R₆, R₇, R₈, and R₁₂) in Schemes 1-10 are as defined in anyof Formulae disclosed herein, unless otherwise specified.

One of ordinary skill in the art will note that, during the reactionsequences and synthetic schemes described herein, the order of certainsteps may be changed, such as the introduction and removal of protectinggroups.

One of ordinary skill in the art will recognize that certain groups mayrequire protection from the reaction conditions via the use ofprotecting groups. Protecting groups may also be used to differentiatesimilar functional groups in molecules. A list of protecting groups andhow to introduce and remove these groups can be found in Greene, T. W.,Wuts, P. G. M., Protective Groups in Organic Synthesis, 3^(rd) edition,John Wiley & Sons: New York, 1999.

Preferred protecting groups include, but are not limited to:

For a hydroxyl moiety: TBS, benzyl, THP, Ac

For carboxylic acids: benzyl ester, methyl ester, ethyl ester, allylester

For amines: Cbz, BOC, DMB

For diols: Ac (x2) TBS (x2), or when taken together acetonides

For thiols: Ac

For benzimidazoles: SEM, benzyl, PMB, DMB

For aldehydes: di-alkyl acetals such as dimethoxy acetal or diethylacetyl.

In the reaction schemes described herein, multiple stereoisomers may beproduced. When no particular stereoisomer is indicated, it is understoodto mean all possible stereoisomers that could be produced from thereaction. A person of ordinary skill in the art will recognize that thereactions can be optimized to give one isomer preferentially, or newschemes may be devised to produce a single isomer. If mixtures areproduced, techniques such as preparative thin layer chromatography,preparative HPLC, preparative chiral HPLC, or preparative SFC may beused to separate the isomers.

The following abbreviations are used throughout the specification andare defined below:

Ac acetyl

AcOH acetic acid

aq. aqueous

BID or b.i.d. bis in die (twice a day)

BOC tert-butoxy carbonyl

Cbz benzyloxy carbonyl

CDCl₃ deuterated chloroform

CH₂Cl₂ dichloromethane

DCM dichloromethane

DMB 2,4 dimethoxy benzyl

DMF N,N-Dimethylformamide

DMSO Dimethyl sulfoxide

EA or EtOAc Ethyl acetate

EDC or EDCI N-(3-Dimethylaminopropyl)-N′-ethylcarbodiimide

ESI− Electrospray negative mode

ESI+ Electrospray positive mode

EtOH ethanol

h hours

H₂O water

HOBt 1-Hydroxybenzotriazole

HCl hydrogen chloride or hydrochloric acid

HPLC High performance liquid chromatography

K₂CO₃ potassium carbonate

LC/MS or LC-MS Liquid chromatography mass spectrum

M Molar

MeCN Acetonitrile

min minutes

Na₂CO₃ sodium carbonate

Na₂SO₄ sodium sulfate

NaHCO₃ sodium bicarbonate

NaHMDs Sodium hexamethyldisilazide

NaOH sodium hydroxide

NaHCO₃ sodium bicarbonate

Na₂SO₄ sodium sulfate

NMR Nuclear Magnetic Resonance

Pd(OH)₂ Palladium dihydroxide

PMB para methoxybenzyl

p.o. per os (oral adinsitration)

ppm parts per million

prep HPLC preparative High Performance Liquid Chromatography

PYBOP (Benzotriazol-1-yloxy)tripyrrolidinophosphoniumhexafluorophosphate

Rt or RT Room temperature

TBME tert-Butyl methyl ether

TFA trifluoroacetic acid

THF tetrahydrofuran

THP tetrahydropyran

The present invention also provides pharmaceutical compositionscomprising a compound of any Formula disclosed herein in combinationwith at least one pharmaceutically acceptable excipient or carrier.

A “pharmaceutical composition” is a formulation containing the compoundsof the present invention in a form suitable for administration to asubject. In one embodiment, the pharmaceutical composition is in bulk orin unit dosage form. The unit dosage form is any of a variety of forms,including, for example, a capsule, an IV bag, a tablet, a single pump onan aerosol inhaler or a vial. The quantity of active ingredient (e.g., aformulation of the disclosed compound or salt, hydrate, solvate orisomer thereof) in a unit dose of composition is an effective amount andis varied according to the particular treatment involved. One skilled inthe art will appreciate that it is sometimes necessary to make routinevariations to the dosage depending on the age and condition of thepatient. The dosage will also depend on the route of administration. Avariety of routes are contemplated, including oral, pulmonary, rectal,parenteral, transdermal, subcutaneous, intravenous, intramuscular,intraperitoneal, inhalational, buccal, sublingual, intrapleural,intrathecal, intranasal, and the like. Dosage forms for the topical ortransdermal administration of a compound of this invention includepowders, sprays, ointments, pastes, creams, lotions, gels, solutions,patches and inhalants. In one embodiment, the active compound is mixedunder sterile conditions with a pharmaceutically acceptable carrier, andwith any preservatives, buffers, or propellants that are required.

As used herein, the phrase “pharmaceutically acceptable” refers to thosecompounds, anions, cations, materials, compositions, carriers, and/ordosage forms which are, within the scope of sound medical judgment,suitable for use in contact with the tissues of human beings and animalswithout excessive toxicity, irritation, allergic response, or otherproblem or complication, commensurate with a reasonable benefit/riskratio.

“Pharmaceutically acceptable excipient” means an excipient that isuseful in preparing a pharmaceutical composition that is generally safe,non-toxic and neither biologically nor otherwise undesirable, andincludes excipient that is acceptable for veterinary use as well ashuman pharmaceutical use. A “pharmaceutically acceptable excipient” asused in the specification and claims includes both one and more than onesuch excipient.

A pharmaceutical composition of the invention is formulated to becompatible with its intended route of administration. Examples of routesof administration include parenteral, e.g., intravenous, intradermal,subcutaneous, oral (e.g., inhalation), transdermal (topical), andtransmucosal administration. Solutions or suspensions used forparenteral, intradermal, or subcutaneous application can include thefollowing components: a sterile diluent such as water for injection,saline solution, fixed oils, polyethylene glycols, glycerine, propyleneglycol or other synthetic solvents; antibacterial agents such as benzylalcohol or methyl parabens; antioxidants such as ascorbic acid or sodiumbisulfite; chelating agents such as ethylenediaminetetraacetic acid;buffers such as acetates, citrates or phosphates, and agents for theadjustment of tonicity such as sodium chloride or dextrose. The pH canbe adjusted with acids or bases, such as hydrochloric acid or sodiumhydroxide. The parenteral preparation can be enclosed in ampoules,disposable syringes or multiple dose vials made of glass or plastic.

A compound or pharmaceutical composition of the invention can beadministered to a subject in many of the well-known methods currentlyused for chemotherapeutic treatment. For example, for treatment ofcancers, a compound of the invention may be injected directly intotumors, injected into the blood stream or body cavities or taken orallyor applied through the skin with patches. The dose chosen should besufficient to constitute effective treatment but not so high as to causeunacceptable side effects. The state of the disease condition (e.g.,cancer, precancer, and the like) and the health of the patient shouldpreferably be closely monitored during and for a reasonable period aftertreatment.

The term “therapeutically effective amount”, as used herein, refers toan amount of a pharmaceutical agent to treat, ameliorate, or prevent anidentified disease or condition, or to exhibit a detectable therapeuticor inhibitory effect. The effect can be detected by any assay methodknown in the art. The precise effective amount for a subject will dependupon the subject's body weight, size, and health; the nature and extentof the condition; and the therapeutic or combination of therapeuticsselected for administration. Therapeutically effective amounts for agiven situation can be determined by routine experimentation that iswithin the skill and judgment of the clinician. In a preferred aspect,the disease or condition to be treated is cancer. In another aspect, thedisease or condition to be treated is a cell proliferative disorder.

For any compound, the therapeutically effective amount can be estimatedinitially either in cell culture assays, e.g., of neoplastic cells, orin animal models, usually rats, mice, rabbits, dogs, or pigs. The animalmodel may also be used to determine the appropriate concentration rangeand route of administration. Such information can then be used todetermine useful doses and routes for administration in humans.Therapeutic/prophylactic efficacy and toxicity may be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., ED₅₀ (the dose therapeutically effective in 50% of thepopulation) and LD₅₀ (the dose lethal to 50% of the population). Thedose ratio between toxic and therapeutic effects is the therapeuticindex, and it can be expressed as the ratio, LD₅₀/ED₅₀. Pharmaceuticalcompositions that exhibit large therapeutic indices are preferred. Thedosage may vary within this range depending upon the dosage formemployed, sensitivity of the patient, and the route of administration.

Dosage and administration are adjusted to provide sufficient levels ofthe active agent(s) or to maintain the desired effect. Factors which maybe taken into account include the severity of the disease state, generalhealth of the subject, age, weight, and gender of the subject, diet,time and frequency of administration, drug combination(s), reactionsensitivities, and tolerance/response to therapy. Long-actingpharmaceutical compositions may be administered every 3 to 4 days, everyweek, or once every two weeks depending on half-life and clearance rateof the particular formulation.

The pharmaceutical compositions containing active compounds of thepresent invention may be manufactured in a manner that is generallyknown, e.g., by means of conventional mixing, dissolving, granulating,dragee-making, levigating, emulsifying, encapsulating, entrapping, orlyophilizing processes. Pharmaceutical compositions may be formulated ina conventional manner using one or more pharmaceutically acceptablecarriers comprising excipients and/or auxiliaries that facilitateprocessing of the active compounds into preparations that can be usedpharmaceutically. Of course, the appropriate formulation is dependentupon the route of administration chosen.

Pharmaceutical compositions suitable for injectable use include sterileaqueous solutions (where water soluble) or dispersions and sterilepowders for the extemporaneous preparation of sterile injectablesolutions or dispersion. For intravenous administration, suitablecarriers include physiological saline, bacteriostatic water, CremophorEL™ (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS). In allcases, the composition must be sterile and should be fluid to the extentthat easy syringeability exists. It must be stable under the conditionsof manufacture and storage and must be preserved against thecontaminating action of microorganisms such as bacteria and fungi. Thecarrier can be a solvent or dispersion medium containing, for example,water, ethanol, polyol (for example, glycerol, propylene glycol, andliquid polyethylene glycol, and the like), and suitable mixturesthereof. The proper fluidity can be maintained, for example, by the useof a coating such as lecithin, by the maintenance of the requiredparticle size in the case of dispersion and by the use of surfactants.Prevention of the action of microorganisms can be achieved by variousantibacterial and antifungal agents, for example, parabens,chlorobutanol, phenol, ascorbic acid, thimerosal, and the like. In manycases, it will be preferable to include isotonic agents, for example,sugars, polyalcohols such as manitol and sorbitol, and sodium chloridein the composition. Prolonged absorption of the injectable compositionscan be brought about by including in the composition an agent whichdelays absorption, for example, aluminum monostearate and gelatin.

Sterile injectable solutions can be prepared by incorporating the activecompound in the required amount in an appropriate solvent with one or acombination of ingredients enumerated above, as required, followed byfiltered sterilization. Generally, dispersions are prepared byincorporating the active compound into a sterile vehicle that contains abasic dispersion medium and the required other ingredients from thoseenumerated above. In the case of sterile powders for the preparation ofsterile injectable solutions, methods of preparation are vacuum dryingand freeze-drying that yields a powder of the active ingredient plus anyadditional desired ingredient from a previously sterile-filteredsolution thereof.

Oral compositions generally include an inert diluent or an ediblepharmaceutically acceptable carrier. They can be enclosed in gelatincapsules or compressed into tablets. For the purpose of oral therapeuticadministration, the active compound can be incorporated with excipientsand used in the form of tablets, troches, or capsules. Oral compositionscan also be prepared using a fluid carrier for use as a mouthwash,wherein the compound in the fluid carrier is applied orally and swishedand expectorated or swallowed. Pharmaceutically compatible bindingagents, and/or adjuvant materials can be included as part of thecomposition. The tablets, pills, capsules, troches and the like cancontain any of the following ingredients, or compounds of a similarnature: a binder such as microcrystalline cellulose, gum tragacanth orgelatin; an excipient such as starch or lactose, a disintegrating agentsuch as alginic acid, Primogel, or corn starch; a lubricant such asmagnesium stearate or Sterotes; a glidant such as colloidal silicondioxide; a sweetening agent such as sucrose or saccharin; or a flavoringagent such as peppermint, methyl salicylate, or orange flavoring.

For administration by inhalation, the compounds are delivered in theform of an aerosol spray from pressured container or dispenser, whichcontains a suitable propellant, e.g., a gas such as carbon dioxide, or anebulizer.

Systemic administration can also be by transmucosal or transdermalmeans. For transmucosal or transdermal administration, penetrantsappropriate to the barrier to be permeated are used in the formulation.Such penetrants are generally known in the art, and include, forexample, for transmucosal administration, detergents, bile salts, andfusidic acid derivatives. Transmucosal administration can beaccomplished through the use of nasal sprays or suppositories. Fortransdermal administration, the active compounds are formulated intoointments, salves, gels, or creams as generally known in the art.

The active compounds can be prepared with pharmaceutically acceptablecarriers that will protect the compound against rapid elimination fromthe body, such as a controlled release formulation, including implantsand microencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters, and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions(including liposomes targeted to infected cells with monoclonalantibodies to viral antigens) can also be used as pharmaceuticallyacceptable carriers. These can be prepared according to methods known tothose skilled in the art, for example, as described in U.S. Pat. No.4,522,811.

It is especially advantageous to formulate oral or parenteralcompositions in dosage unit form for ease of administration anduniformity of dosage. Dosage unit form as used herein refers tophysically discrete units suited as unitary dosages for the subject tobe treated; each unit containing a predetermined quantity of activecompound calculated to produce the desired therapeutic effect inassociation with the required pharmaceutical carrier. The specificationfor the dosage unit forms of the invention are dictated by and directlydependent on the unique characteristics of the active compound and theparticular therapeutic effect to be achieved.

In therapeutic applications, the dosages of the pharmaceuticalcompositions used in accordance with the invention vary depending on theagent, the age, weight, and clinical condition of the recipient patient,and the experience and judgment of the clinician or practitioneradministering the therapy, among other factors affecting the selecteddosage. Generally, the dose should be sufficient to result in slowing,and preferably regressing, the growth of the tumors and also preferablycausing complete regression of the cancer. Dosages can range from about0.01 mg/kg per day to about 5000 mg/kg per day. In preferred aspects,dosages can range from about 1 mg/kg per day to about 1000 mg/kg perday. In an aspect, the dose will be in the range of about 0.1 mg/day toabout 50 g/day; about 0.1 mg/day to about 25 g/day; about 0.1 mg/day toabout 10 g/day; about 0.1 mg to about 3 g/day; or about 0.1 mg to about1 g/day, in single, divided, or continuous doses (which dose may beadjusted for the patient's weight in kg, body surface area in m², andage in years). An effective amount of a pharmaceutical agent is thatwhich provides an objectively identifiable improvement as noted by theclinician or other qualified observer. For example, regression of atumor in a patient may be measured with reference to the diameter of atumor. Decrease in the diameter of a tumor indicates regression.Regression is also indicated by failure of tumors to reoccur aftertreatment has stopped. As used herein, the term “dosage effectivemanner” refers to amount of an active compound to produce the desiredbiological effect in a subject or cell.

The pharmaceutical compositions can be included in a container, pack, ordispenser together with instructions for administration.

The compounds of the present invention are capable of further formingsalts. All of these forms are also contemplated within the scope of theclaimed invention.

As used herein, “pharmaceutically acceptable salts” refer to derivativesof the compounds of the present invention wherein the parent compound ismodified by making acid or base salts thereof. Examples ofpharmaceutically acceptable salts include, but are not limited to,mineral or organic acid salts of basic residues such as amines, alkalior organic salts of acidic residues such as carboxylic acids, and thelike. The pharmaceutically acceptable salts include the conventionalnon-toxic salts or the quaternary ammonium salts of the parent compoundformed, for example, from non-toxic inorganic or organic acids. Forexample, such conventional non-toxic salts include, but are not limitedto, those derived from inorganic and organic acids selected from2-acetoxybenzoic, 2-hydroxyethane sulfonic, acetic, ascorbic, benzenesulfonic, benzoic, bicarbonic, carbonic, citric, edetic, ethanedisulfonic, 1,2-ethane sulfonic, fumaric, glucoheptonic, gluconic,glutamic, glycolic, glycollyarsanilic, hexylresorcinic, hydrabamic,hydrobromic, hydrochloric, hydroiodic, hydroxymaleic, hydroxynaphthoic,isethionic, lactic, lactobionic, lauryl sulfonic, maleic, malic,mandelic, methane sulfonic, napsylic, nitric, oxalic, pamoic,pantothenic, phenylacetic, phosphoric, polygalacturonic, propionic,salicyclic, stearic, subacetic, succinic, sulfamic, sulfanilic,sulfuric, tannic, tartaric, toluene sulfonic, and the commonly occurringamine acids, e.g., glycine, alanine, phenylalanine, arginine, etc.

Other examples of pharmaceutically acceptable salts include hexanoicacid, cyclopentane propionic acid, pyruvic acid, malonic acid,3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, 4-chlorobenzenesulfonicacid, 2-naphthalenesulfonic acid, 4-toluenesulfonic acid,camphorsulfonic acid, 4-methylbicyclo-[2.2.2]-oct-2-ene-1-carboxylicacid, 3-phenylpropionic acid, trimethylacetic acid, tertiary butylaceticacid, muconic acid, and the like. The present invention also encompassessalts formed when an acidic proton present in the parent compound eitheris replaced by a metal ion, e.g., an alkali metal ion, an alkaline earthion, or an aluminum ion; or coordinates with an organic base such asethanolamine, diethanolamine, triethanolamine, tromethamine,N-methylglucamine, and the like. In the salt form, it is understood thatthe ratio of the compound to the cation or anion of the salt can be 1:1,or any ration other than 1:1, e.g., 3:1, 2:1, 1:2, or 1:3.

It should be understood that all references to pharmaceuticallyacceptable salts include solvent addition forms (solvates) or crystalforms (polymorphs) as defined herein, of the same salt.

The compounds of the present invention can also be prepared as esters,for example, pharmaceutically acceptable esters. For example, acarboxylic acid function group in a compound can be converted to itscorresponding ester, e.g., a methyl, ethyl or other ester. Also, analcohol group in a compound can be converted to its corresponding ester,e.g., acetate, propionate or other ester.

The compounds, or pharmaceutically acceptable salts or solvates thereof,are administered orally, nasally, transdermally, pulmonary,inhalationally, buccally, sublingually, intraperintoneally,subcutaneously, intramuscularly, intravenously, rectally,intrapleurally, intrathecally and parenterally. In one embodiment, thecompound is administered orally. One skilled in the art will recognizethe advantages of certain routes of administration.

The dosage regimen utilizing the compounds is selected in accordancewith a variety of factors including type, species, age, weight, sex andmedical condition of the patient; the severity of the condition to betreated; the route of administration; the renal and hepatic function ofthe patient; and the particular compound or salt thereof employed. Anordinarily skilled physician or veterinarian can readily determine andprescribe the effective amount of the drug required to prevent, counter,or arrest the progress of the condition.

Techniques for formulation and administration of the disclosed compoundsof the invention can be found in Remington: the Science and Practice ofPharmacy, 19^(th) edition, Mack Publishing Co., Easton, Pa. (1995). Inan embodiment, the compounds described herein, and the pharmaceuticallyacceptable salts thereof, are used in pharmaceutical preparations incombination with a pharmaceutically acceptable carrier or diluent.Suitable pharmaceutically acceptable carriers include inert solidfillers or diluents and sterile aqueous or organic solutions. Thecompounds will be present in such pharmaceutical compositions in amountssufficient to provide the desired dosage amount in the range describedherein.

All percentages and ratios used herein, unless otherwise indicated, areby weight. Other features and advantages of the present invention areapparent from the different examples. The provided examples illustratedifferent components and methodology useful in practicing the presentinvention. The examples do not limit the claimed invention. Based on thepresent disclosure the skilled artisan can identify and employ othercomponents and methodology useful for practicing the present invention.

In the synthetic schemes described herein, compounds may be drawn withone particular configuration for simplicity. Such particularconfigurations are not to be construed as limiting the invention to oneor another isomer, tautomer, regioisomer or stereoisomer, nor does itexclude mixtures of isomers, tautomers, regioisomers or stereoisomers;however, it will be understood that a given isomer, tautomer,regioisomer or stereoisomer may have a higher level of activity thananother isomer, tautomer, regioisomer or stereoisomer.

Compounds designed, selected and/or optimized by methods describedabove, once produced, can be characterized using a variety of assaysknown to those skilled in the art to determine whether the compoundshave biological activity. For example, the molecules can becharacterized by conventional assays, including but not limited to thoseassays described below, to determine whether they have a predictedactivity, binding activity and/or binding specificity.

Furthermore, high-throughput screening can be used to speed up analysisusing such assays. As a result, it can be possible to rapidly screen themolecules described herein for activity, using techniques known in theart. General methodologies for performing high-throughput screening aredescribed, for example, in Devlin (1998) High Throughput Screening,Marcel Dekker; and U.S. Pat. No. 5,763,263. High-throughput assays canuse one or more different assay techniques including, but not limitedto, those described below.

An EZH2 inhibitor of the present invention may, if desired, be presentedin a kit (e.g., a pack or dispenser device) which may contain one ormore unit dosage forms containing the EZH2 inhibitor. The pack may forexample comprise metal or plastic foil, such as a blister pack. The packor dispenser device may be accompanied by instructions foradministration. Compositions comprising an EZH2 inhibitor of theinvention formulated in a compatible pharmaceutical carrier may also beprepared, placed in an appropriate container, and labeled for treatmentof an indicated condition. Instructions for use may also be provided.

Also provided herein are kits comprising a plurality of methylationdetection reagents that detect the methylated H3-K27. For example, thekit includes mono-methylated H3-K27, di-methylated H3-K27 andtri-methylated H3-K27 detection reagents. The detection reagent is forexample antibodies or fragments thereof, polypeptide or aptamers.

A kit may also include reagents for detecting loss of function of atleast one component of the SWI/SNF complex, e.g., nucleic acids thatspecifically identify a mutant component nucleic acid sequence by havinghomologous nucleic acid sequences, such as oligonucleotide sequences,complementary to a portion of the mutant component nucleic acid sequenceor antibodies to proteins encoded by the wild type and/or mutantcomponent nucleic acids packaged together in the form of a kit. Theoligonucleotides can be fragments of the component gene. For example theoligonucleotides can be 200, 150, 100, 50, 25, 10 or less nucleotides inlength. The kit may contain in separate containers an aptamer or anantibody, control formulations (positive and/or negative), and/or adetectable label such as fluorescein, green fluorescent protein,rhodamine, cyanine dyes, Alexa dyes, luciferase, radiolabels, amongothers. In addition, reagents for detecting the biological activity ofthe SWI/SNF complex (such as its chromatin remodeling activity) may beincluded in the kit.

Instructions (e.g., written, tape, VCR, CD-ROM, etc.) for carrying outthe assay may be included in the kit. The assay may for example be inthe form of a Western Blot analysis, Immunohistochemistry (IHC),immunofluorescence (IF), sequencing and Mass spectrometry (MS) as knownin the art.

Example 1: Durable Tumor Regression in Genetically Altered Lymphomas andMalignant Rhabdoid Tumors by Inhibition of EZH2

Compound A is a Potent and Selective Inhibitor of EZH2:

Cell free biochemical assays that included radiolabeled SAM and eitherchicken erythrocyte oligonucleosomes or peptides corresponding to H3K27as substrates showed that Compound A selectively inhibited the activityof human PRC2 containing wild-type EZH2 with an inhibition constant (Ki)value of 2.5±0.5 nmol/L and IC₅₀ values of 11±5 nM (nucleosome assay) or16±12 nM (peptide assay). The IC₅₀ values were similar for human and ratEZH2 enzymes as well as for EZH2 proteins bearing all known lymphomachange-of-function mutations. The IC₅₀ value of Compound A increasedwith increasing concentration of SAM, but was minimally affected byincreasing the amount of oligonucleosome which is consistent with aSAM-competitive and nucleosome-noncompetitive modality of inhibition. Inorder to demonstrate HMT selectivity, inhibition by Compound A against apanel of HMTs other than EZH2 encompassing both lysine and arginine HMTswas assessed. Compound A displayed a 35-fold selectivity versus EZH1 andgreater than 4500-fold selectivity relative to the 14 other HMTs tested.

Compound A Specifically Inhibits Cellular H3K27 Methylation in Cells:

When WSU-DLCL2 EZH2 Y641F mutant lymphoma cells were incubated withCompound A for 4 days, a concentration-dependent reduction in globalH3K27Me3 levels was observed with an average IC₅₀ value of 0.26 μM(H3K27Me3 levels determined by ELISA). When studying the kinetics ofmethylation inhibition, the half-life of H3K27Me3 was approximately 1day as 90% inhibition was only achieved after 3 to 4 days of incubation.When OCI-LY19 EZH2 wild-type lymphoma cells were incubated with 2.7 μMCompound A for 4 days, the only methyl marks affected were the H3K27Me1,H3K27Me2 and H3K27Me3, the three known products of PRC2 catalysis.Incubation with Compound A also resulted in an increase in H3K27acetylation. The ability of Compound A to reduce global H3K27trimethylation levels was further tested in several other human lymphomacell lines including lines expressing either wild-type or mutant EZH2.Compound A reduced H3K27Me3 with similar potency in all cell linesindependent of the EZH2 status (Table 1).

Compound A Leads to Selective Killing of Lymphoma Cell Lines BearingEZH2 Point Mutations:

Incubation of WSU-DLCL2 EZH2 Y641F mutant cells with Compound A lead toanti-proliferative effects with an average IC₅₀ value of 0.28±0.14 μM ina 6 day proliferation assay. The kinetics of the effect of Compound A onviable cell number was further tested over an extended period of 11days. The antiproliferative effect of Compound A was apparent afterWSU-DLCL2 cells had been exposed to compound for longer than 4 days,consistent with the kinetics of Compound A-mediated cellular H3K27methylation inhibition. The IC₅₀ value for Compound A inhibition ofproliferation of WSU-DLCL2 cells in the 11-day assay (0.0086 μM,Table 1) was lower when compared with results obtained with a 6-dayproliferation assay, suggesting increased sensitivity with longerincubation periods. In contrast to the WSU-DLCL2 cells, the growth ofOCI-LY19 human lymphoma cells (EZH2 wild type for residue Y641) over 11days was not significantly affected, despite comparable IC₅₀ values forH3K27Me3 inhibition for both cell lines (Table 1). In order to identifya concentration at which cells stop proliferating considering the entireincubation period of 11 days, the lowest cytotoxic concentration (LCC)for a particular cell line was calculated. The LCC value for WSU-DLCL2EZH2 Y641F mutant human lymphoma cells was significantly lower whencompared with OCI-LY19 cells that are wild type for EZH2 (Table 1). Thiscontext specific cell killing was further supported by results from11-day proliferation assays with an extended lymphoma cell line panel.All cell lines harboring an EZH2 mutation, with the exception of the RLcell line (EZH2 Y641N), were more sensitive to the antiproliferativeeffects of Compound A when compared with cell lines with wild-type EZH2(Table 1). The Pfeiffer cell line (EZH2 A677G) showed a 20 to 300 foldincrease in sensitivity to Compound A, as measured by IC₅₀ value andLCC, respectively, over the Y641 mutant cell lines. Next the minimumtime of compound exposure necessary for sustained cell killing wasinvestigated by washout experiments. The LCC values on day 11 or 14 forWSU-DLCL2cells that were either incubated with Compound A for 7 days(followed by 7 days of compound washout) or continuously for 14 dayswere similar (Table 2). Drug exposure for only 4 days, however, was notsufficient to induce LCC values similar to continuous incubation.

Compound A Induces G₁ Arrest and Apoptosis in EZH2 Mutant LymphomaCells:

Next, the effects of incubation with Compound A (1 μM) for 7 days oncell cycle progression and apoptosis in WSU-DLCL2 cells were assessed.An increase in the percentage of cells in G₁ phase, and a decrease inthe percentage of cells in S phase and G2/M phase was apparent after 2days of Compound A incubation. The maximum effect was achieved after 4days. There was no apparent increase in the sub-G₁ fraction suggestingthat apoptosis was not induced by Compound A incubation for 7 days. Thisis in agreement with the growth curves of WSU-DLCL2 cells in thepresence of Compound A indicating that cytotoxic effects were observedonly after 7 days of incubation. Following incubation of WSU-DLCL2 cellswith Compound A for up to 14 days, the fraction of apoptotic cellsdetermined by TUNEL assay was significantly increased on day 14 comparedto vehicle, indicating that Compound A-mediated cell death occurredthrough the induction of apoptosis.

Oral Administration of Compound A Leads to EZH2 Target Inhibition inEZH2 Mutant Xenograft Models in Mice:

The effect of oral dosing of Compound A on systemic compound exposureand in vivo target inhibition in mice bearing EZH2 mutant lymphomaxenografts was investigated. First, SCID mice implanted subcutaneouslywith WSU-DLCL2 xenografts were orally dosed with Compound A for 4 or 7days. Measuring Compound A plasma levels either 5 minutes before or 3hours after the last dose revealed a clear dose dependent increase inexposure. Only animals dosed at 160 mg/kg TID or 213 mg/kg BIDmaintained mean compound levels in plasma above the LCC for WSU-DLCL2cells throughout a dosing cycle (1652 ng/mL, with mouse plasma proteinbinding considered). Compound determination in homogenates from tumorscollected 3 hours after the last dose revealed that only for the highestdose groups compound levels in the 2 compartments were similar. WhenH3K27Me3 levels in tumors were analyzed, dose dependent EZH2 targetinhibition was observed. H3K27Me3 inhibition was less in tumors frommice dosed at 213 mg/kg QD, suggesting that maintaining a plasmaconcentration above LCC throughout a dosing cycle is required foroptimal target inhibition. Dosing for 4 days at 160 mg/kg TID resultedin slightly lower target inhibition than dosing for 7 days at the samedose and schedule, indicating that prolonged dosing increased the degreeof target inhibition in WSU-DLCL2 tumors. A similar 7-day study in nudemice implanted subcutaneously with KARAPS-422 xenografts assessing bothBID and QD schedules was performed. Compound A induced a dose-dependentreduction of tumor H3K27Me3 levels at both regimens.

Compound A Induces Significant Antitumor Effects in Several EZH2 MutantLymphoma Xenografts:

When WSU-DLCL2 EZH2 Y641F mutant xenograft tumor bearing SCID mice weretreated with Compound A for 28 days, dose-dependent tumor growthinhibition, 58% at the highest dose of 150 mg/kg TID, was observed. Onlyanimals administered the highest dose maintained mean Compound A plasmalevels above LCC for WSU-DLCL2 cells throughout the dosing cycle. Dosingof Compound A for 28 days led to a relative compound accumulation intumor tissue compared with plasma, in contrast to what was observed with7-day dosing. ELISA analysis of histones from tumors collected on day 28indicated dose-dependent target inhibition. H3K27Me3 levels in WSU-DLCL2xenografts were lower in mice dosed for 28 days compared with 7 daysindicating that prolonged administration of Compound A increased thedegree of target inhibition. In KARPAS-422 EZH2 Y461N mutant xenografts,28-day dosing of Compound A on a BID schedule had much more dramaticeffects. Tumor growth inhibition was observed at doses as low as 80.5mg/kg BID, but higher doses eradicated the xenografts, and no re-growthwas observed for up to 90 days after cessation of dosing. Whenintermittent dosing schedules were investigated in KARPAS-422 xenograftbearing mice, Compound A again showed significant dose-dependentantitumor effects with two cycles of 7-day on/7-day off and 21 day on/7day off schedules. For all dosing schedules, tumor growth inhibition andcomplete regressions were observed at 90 and 361 mg/kg BID,respectively. The Pfeiffer EZH2 A677G mutant xenograft model was themost sensitive tumor model, as suggested by the potentanti-proliferative effects of Compound A on this cell line in vitro. AllCompound A dose groups (QD schedule) except the lowest one (30 mg/kg QD)showed complete tumor regressions in all animals. Again, tumor re-growthwas not observed until the end of the study (36 days after stoppingCompound A administration). Although tumor re-growth was observed at 30mg/kg QD, this very low dose induced tumor stasis during theadministration period. Due to tolerability issues dosing was stopped onday 12 for mice administered 1140 mg/kg QD; still, durable completeregressions were observed in this group that were only exposed toCompound A for 12 days.

Compound A Selectively Kills SMARCB1 Mutant MRT Cells In Vitro and inVivo:

Whether EZH2 inhibition had any effects on the growth and survival ofSMARCB1-deleted MRT cells was tested. Incubating SMARCB1-deleted MRTcell lines G401 and A204 with Compound A in a 14-day proliferation assayin vitro induced strong anti-proliferative effects with IC₅₀ values inthe nM range while the control cell lines RD and SJCRH30 which expressedSMARCB1 were minimally affected (Table 3). Dosing of SCID mice bearingsubcutaneous G401 xenografts with Compound A at 266 or 532 mg/kg BID for28 days eliminated those extremely fast growing tumors. Similar to theKARPAS-422 and Pfeiffer EZH2 mutant NHL xenograft models re-growth wasnot observed at study end, 32 days after dosing stop. Compound A dosedat 133 mg/kg induced stasis during the administration period, andproduced a significant tumor growth delay compared to vehicle afterdosing stop. Tumors that were harvested from subsets of mice from eachgroup on day 21 showed strong EZH2 target inhibition at all doses.

Compound A Inhibits H3K27 Methylation in Nontumor Tissues in a DoseDependent Manner:

The data described above demonstrate that Compound A represents a newtreatment modality for SWI/SNF driven cancers and MRTs. Measuringpharmacodynamic biomarker modulation post-dose is often performed inearly clinical trials to assess the degree of target inhibition that ispredicted to produce a response based on data from preclinical models.Since the collection of post-dose tumor biopsies is often not possible,easier accessible surrogate tissues such as peripheral blood mononuclearcells (PBMCs), skin or bone marrow are often collected instead. To testEZH2 target inhibition in surrogate tissues male and female SpragueDawley rats were orally administered 100, 300, or 1000 mg/kg Compound Afor 28 days, and PBMCs, bone marrow and skin samples were collected atstudy end. Plasma levels of Compound A increased dose-dependently inboth male and female rats, and the plasma levels were generally higherin females compared with those in males. Due to tolerability issues,females in the 1000 mg/kg group had to be euthanized on day 23.Dose-dependent target inhibition was observed in PBMCs and bone marrowfrom rats dosed with Compound A, as measured by ELISA. The degree oftarget inhibition was less pronounced for PBMCs from females that weredosed for 22 days compared with males that were dosed for 28 days (samedose of 1000 mg/kg). A dose dependent reduction in H3K27Me3 positivecells was observed in the epidermis of skin of Compound A-dosed rats, asassessed by an IHC assay. The maximum effect was observed at the highestdose, and was already evident after 22 days of Compound Aadministration.

Compound A displayed similar properties as other EZH2 inhibitors invitro, such as very high specificity for EZH2 in biochemical assays whencompared with other HMTs and specific inhibition of cellular H3K27methylation leading to context specific killing of EZH2 mutated NHL celllines. However, this compound achieved an approximately 10-fold increasein potency, reflected by decreased K_(i) and IC₅₀ values determined inbiochemical and cell-functional assays. In addition, Compound A showedexcellent oral bioavailability when administered to rodents which leadto dose dependent EZH2 target inhibition in xenograft tumor and nontumortissues. Importantly, dosing of Compound A induced significant antitumoreffects in mice bearing EZH2 mutant lymphoma xenografts. The responsesranged from tumor eradication (no regrowth after dosing cessation) todose-dependent tumor growth inhibition. The delayed onset of antitumoractivity (after 4 to 7 days) was consistent with the kinetics ofmethylation inhibition and antiproliferative activity induced byincubation of cells with Compound A in vitro. Keeping Compound A plasmalevels above LCC throughout a dosing cycle was necessary for theWSU-DLCL2 xenograft model to induce maximal target inhibition andantitumor response. The other two lymphoma xenograft models (KARPAS-422and Pfeiffer), however, were extremely sensitive to Compound Aadministration, and keeping plasma levels above LCC was not necessary.Pfeiffer EZH2 A677G mutant xenograft tumors disappeared permanently withvery low doses or short dosing periods, suggesting that patients withthis type of genetically defined NHL would have a significant treatmenteffect with Compound A.

MRTs are extremely aggressive pediatric cancers of the brain, kidney,and soft tissues that are highly malignant, locally invasive, frequentlymetastatic, and particularly lethal, but they are typically diploid andlack genomic aberrations. They are, however, characterized by an almostcomplete penetrance of loss of expression of the SMARCB1, a corecomponent of the SWI/SNF chromatin remodeling complex. The biallelicinactivation of SMARCB1, for instance induced by mutations, is inessence the sole genetic event in MRTs which suggests a driver role forthis genetic aberration. Through genetic studies it has been suggestedthat PRC2 and SWI/SNF antagonistically regulate gene expression aroundthe RB, Cyclin D1 and MYC pathways. Here, it has been demonstratedpharmacological EZH2 inhibition induced antiproliferative effects inSMARCB1 deleted MRT cell lines and permanently eradicated MRT xenograftsin mice. This confirms the dependency of such cancers, in which EZH2itself is not genetically altered, on PRC2 activity.

Compound A represents a new treatment modality for genetically definedsubsets of NHL and for MRTs. The ability to measure dose-dependentchanges in H3K27Me3 levels in skin, PBMCs and bone marrow portends theuse of signal from these surrogate tissues as a non-invasivepharmacodynamics biomarker in human clinical trials.

TABLE 1 IC₅₀ Values for Methylation and Proliferation as well as LCCValues for Compound A in Human Lymphoma Cell Lines MethylationProliferation IC₅₀ IC₅₀ LCC Cell Line EZH2 Status (nmol/L)^(a)(μmol/L)^(b) (μmol/L)^(b) DOHH-2 Wild Type ND 1.7 >10 Farage Wild TypeND 0.099 >10 OCI-LY19 Wild Type  8 6.2 10-25 Toledo Wild Type ND 7.6 >10Karpas-422 Y641N 90 0.0018 0.12 Pfeiffer A677G  2 0.00049 0.0005 RLY641N 22 5.8 >25 SU-DHL-10 Y641F ND 0.0058 0.14 SU-DHL-6 Y641N 20 0.00470.21 WSU-DLCL2 Y641F  9 0.0086 0.17 ^(a)Derived after incubation for 4days by immunoblot. Values represent the result from one experiment.^(b)Derived after incubation for 11 days. Compound incubations for eachexperiment were performed in triplicate, and values represent oneexperiment for all cell lines except OCI-LY19, Pfeiffer, and WSU-DLCL2.For the remaining three cell lines, values represent the mean from thefollowing number of experiments: OCI-LY19 n = 9; Pfeiffer n = 2 andWSU-DLCL2 n = 15.

TABLE 2 LCC Values for Compound A for WSU-DLCL2 Human Lymphoma CellsDosed Either Continuously or After Compound Washout Day 11 Day 14 LCCLCC WSU-DLCL2 Washout (μM) (μM) No Washout 0.17 0.11 4-day Compound A;0.36 0.42 11-day Washout 7-day Compound A; 0.19 0.075 7-day WashoutValues represent the mean of duplicate experiments with three replicatesper incubation concentration within the experiments.

TABLE 3 IC₅₀ Values for Compound A for SMARCB1 Negative MRT Cell Linesand SMARCB1 Positive Control Cell Lines Proliferation ProliferationSMARCB1 IC₅₀ (μM), IC₅₀ (μM), Cell Line Status day 7 day 14 RD Wild Type9.2 5.2 SJCRH30 Wild Type 6.1 8.8 G401 Mutant 0.087 0.042 A204 Mutant3.2 0.14 Values represent the mean of duplicate experiments with threereplicates per incubation concentration within the experiments.

Example 2: Durable Tumor Regression in Genetically Altered MalignantRhabdoid Tumors by Inhibition of EZH2

Compound A is a Potent and Selective Inhibitor of EZH2:

Compound A was developed through iterative medicinal chemistry (FIG.10A). Compound A inhibited the activity of human PRC2 containingwild-type EZH2 with an inhibition constant (K_(i)) value of 2.5±0.5 nM,and similar potency was observed for EZH2 proteins bearing all knownlymphoma change-of-function mutations (Table 5). The compound was foundto be SAM-competitive and nucleosome-noncompetitive by steady statekinetic studies (FIG. 11). Inhibition by Compound A against a panel ofHMTs other than EZH2 encompassing both lysine and arginine HMTs was alsoassessed. Compound A displayed a 35-fold selectivity versus EZH1and >4500-fold selectivity relative to 14 other HMTs tested (Table 5).

TABLE 4 Histone Methyltransferase Inhibition by Compound A IC₅₀ %Inhibition at Enzyme Assay (nM) 1 μM Compound A^(a) CARM1 >50,000^(b) 5± 3 DOT1L >50,000^(c) 2 ± 8 EHMT1 >50,000^(c) 6 ± 6 EHMT2 >50,000^(c) 7± 3 EZH1^(d,e) 392 ± 72^(f) 98 ± 1  EZH2 Peptide 11 ± 5^(f) NDAssay^(d,e) EZH2 Nucleosome  16 ± 12^(f) 100 ± 1  Assay^(d) A677GEZH2^(d,e)     2^(b) ND A687V EZH2^(d,e)     2^(b) ND Y641F EZH2^(d,e)14 ± 5^(f) ND Y641C EZH2^(d,e)    16^(c) ND Y641H EZH2^(d,e)     6^(c)ND Y641N EZH2^(d,e)    38^(b) ND Y641S EZH2^(d,e)     6^(c) ND ratEZH2^(d,e)     4^(c) ND PRMT1 >50,000^(c) 5 ± 4 PRMT3 ND 2 ± 2PRMT5/MEP50 >50,000^(c) 2 ± 6 PRMT6 ND 3 ± 3 PRMT8 >50,000^(c) 7 ± 3SETD7 ND 4 ± 3 SMYD2 >50,000^(c) 1 ± 2 SMYD3 ND 0 ± 5 WHSC1>100,000^(c)  8 ± 3 WHSC1L1 >100,000^(c)  9 ± 8 ^(a)Values represent themean and standard deviation of duplicate experiments determined at 10μmol/L Compound A. ^(b)Values represent the mean of duplicateexperiments with two replicates per experiment. ^(c)Values represent oneexperiment with two replicates per experiment. ^(d)All EZH1 and EZH2proteins were assayed in the context of 4 PRC2 components (EZH1/2,SUZ12, RBAP48, EED). ^(e)Assayed with H3K27 peptides as substrates.

Compound A Specifically Inhibits Cellular H3K27 Methylation Leading toSelective Apoptotic Killing of SMARCB1 Mutant MRT Cells:

A panel of SMARCB1 deficient MRT cells and SMARM wild-type control cells(confirmed by immunoblot, FIG. 12A) were treated with Compound A for 4days, resulting in concentration-dependent reductions in global H3K27Me3levels (FIG. 10B and table 6). Treatment of either wild-type or mutantcells resulted in diminution only of methyl marks on H3K27, with noother histone methyl marks being affected (FIG. 12B). In vitro treatmentof SMARCB1-deleted MRT cell lines with Compound A induced stronganti-proliferative effects with IC₅₀ values in the nM range; while thecontrol (wild-type) cell lines were minimally affected (FIG. 10C andtable 6). Antiproliferative effects were apparent in SMARCB1-deleted MRTcells after 7 days of compound exposure, but required 14 days ofexposure for maximal activity. The effects of incubation with Compound A(1 μM) for 14 days on cell cycle progression and apoptosis in G401 andRD cells were also assessed. Compound A incubation of RD SMARCB1wild-type cells showed no changes in cell cycle or apoptosis compared tothe DMSO control (FIG. 13A). In contrast, G401 SMARCB1-deleted cellsshowed an increase in the percentage of cells in G₁ phase, and aconcomitant decrease in S phase and G2/M phase after 7 days (FIG. 13B).There was no apparent increase in the sub-G₁ fraction through day 7,suggesting that apoptosis was not yet induced by that time. Thiscoincides with the growth curves of G401 cells in the presence ofCompound A that display cytotoxicity only after 7 days of incubation(FIG. 10C). Following Compound A treatment of G401 cells for up to 14days, the fraction of cells in sub-G₁ as well as apoptotic cellsdetermined by TUNEL assay increased in a time dependent manner throughdays 11 and 14, indicating that Compound A-mediated cell death occurredthrough the induction of apoptosis (FIG. 13B).

TABLE 6 Proliferation SMARCB1 Methylation IC₅₀ on Day Cell Line StatusIC₅₀ (nM)^(a) 14 (nM)^(b) G401 mutant 2.7 135 A204 mutant 1.4 590 G402mutant 1.7 144 KYM-1 mutant 4.3 32 RD wild-type 5.6 6100, >10000^(c) 293wild-type 2.4 >10000 SJCRH30 wild-type 4.9 5100. >10000^(c) ^(a)Derivedafter incubation for 4 days, extraction of histones, immunoblot anddensitometry. Values represent the mean from two experiments.^(b)Compound incubations for each experiment were performed intriplicate, and values represent the mean of 2 experiments for all celllines. ^(c)Mean calculation of duplicate experiment not possible.

Compound A Induces Genes of Neuronal Differentiation and Cell CycleInhibition while Suppressing Expression of Hedgehog Pathway Genes, MYCand EZH2:

It has been suggested that SMARCB1 loss drives cancer formation throughsimultaneous epigenetic perturbation of key cancer pathways. The presentdata confirmed the previously described reduced expression of genesimportant for neuronal differentiation (CD133, DOCK4, PTPRK), cell cycleinhibition (CDKN2A) and tumor suppression (BIN1), as well as increasedexpression of the hedgehog pathway gene GLI1 in SMARCB1-deleted G401cells compared to control cells (FIG. 14A). Compound A treatment of G401cells for up to 7 days strongly induced expression of CD133, DOCK4 andPTPRK and up-regulated cell cycle inhibitors CDKN1A and CDKN2A and tumorsuppressor BIN1, all in a time-dependent manner (FIG. 14B).Simultaneously, the expression of hedgehog pathway genes, MYC and EZH2were reduced. Notably, G402 SMARCB1-deleted cells exposed to Compound Afor 14 days assumed a neuron-like morphology (FIG. 14C). In contrast,Compound A incubation of RD control cells had minimal effect onexpression of the above-mentioned genes.

Compound A Eradicates SMARCB1 Mutant MRT Xenografts:

Oral dosing of Compound A led to systemic compound exposure, in vivotarget inhibition and antitumor activity in mice bearing SMARCB1-deletedMRT xenografts. A study in SCID mice bearing subcutaneous G401xenografts was performed where animals were dosed for 21 days withCompound A. Half of the mice per group were euthanized on day 21 tocollect blood and tissues, while the remaining animals were treated foran additional 7 days and then left without dosing for another 32 days.Compound A was well tolerated at all doses with minimal effect on bodyweight (FIG. 15A). Dosing at 250 or 500 mg/kg twice daily (BID) for 21to 28 days practically eliminated the fast-growing G401 tumors (FIGS.15B, 14C and 16A). R_(e)-growth was not observed for 32 days after dosecessation. Compound A dosed at 125 mg/kg induced tumor stasis during theadministration period, and produced a significant tumor growth delaycompared to vehicle after the dosing period. Measuring Compound A plasmalevels either 5 min before or 3 h after dosing on day 21 revealed aclear dose-dependent increase in systemic exposure (FIG. 15D). Tumorsthat were harvested from subsets of mice from each group on day 21showed strong inhibition of H3K27me3, correlating with the antitumoractivity (maximum effect achieved at 250 mg/kg, FIG. 16B). In addition,dose-dependent changes in the expression of CD133, PTPRK, DOCK4 and GLI1were detected in the G401 xenograft tumors (FIG. 16C).

The present data demonstrate that pharmacological inhibition of EZH2induced antiproliferative effects specifically in SMARCB1-deleted MRTcell lines and permanently eradicated MRT xenografts in mice. Thisconfirms the dependency of such cancers on PRC2 activity, despite thefact that EZH2 itself is not genetically altered in this context. Datapresented herein show that in the context of SMARCB1-deleted MRT,inhibition of EZH2 functions as a SMARCB1 surrogate and de-repressesneuronal differentiation genes, cell cycle inhibitors and tumorsuppressors while reducing GLI1, PTCH1, MYC and EZH2. The sum of theeffects of Compound A mediated EZH2 inhibition on several cancerpathways is the cause for the dramatic and permanent anti-tumor activityseen in MRT models. Thus, Compound A represents a new treatment modalityfor these lethal childhood tumors.

Furthermore, since several members of the SWI/SNF complex aregenetically altered in other cancer types besides MRT, it is conceivablethat EZH2 also plays a role in tumor maintenance and survival in aspectrum of cancer types. Combined with recent reports demonstrating theeffectiveness of EZH2 inhibitors in selective killing of EZH2 mutantbearing non-Hodgkin lymphomas, the present data demonstrate that smallmolecule-based inhibition of EZH2 is an effective mechanism oftherapeutic intervention in a variety of hematologic and solid tumorsfor which genetic alterations—either target-directed or indirect—confera proliferative dependency on EZH2 enzymatic activity.

Example 3: Material and Methods

Cell Culture:

Cell lines 293T, RD, SJCRH30, A204, G401, G402, and KYM-1. 293T(CRL-11268), RD (CRL-136), SJCRH30 (CRL-2061), A204 (HTB-82), G401(CRL-1441), and G402 (CRL-1440) were obtained from ATCC. KYM-1(JCRB0627) was obtained from JCRB. 293T and RD cells were cultured inDMEM+10% FBS. SJCRH30 cells were cultured in RPMI+10% FBS. A204, G401,and G402 cells were cultured in McCoys 5a+10% FBS. KYM-1 cells werecultured in DMEM/Ham's F12+10% FBS.

Western Blots Analysis:

Histones were acid extracted as previously described (Daigle et al.,Blood. 2013 Aug. 8; 122(6):1017-25). Western blots for acid extractedhistones were performed as previously described (Knutson et al., ProcNatl Acad Sci USA. 2013 May 7; 110(19):7922-7). Whole cell lysates (WCL)were prepared using a modified RIPA buffer (10×RIPA Lysis Buffer(Millipore #20-188), 0.1% SDS (Invitrogen AM9823), protease mini-tablet(Roche #1836153)). Cells were pelleted, washed with ice cold PBS,resuspended in ice cold RIPA buffer, and incubated on ice for 5 minutes.Lysates were sonicated 3× for 10 sec at 50% power, then incubated on icefor 10 minutes. Lysates were then centrifuged at max speed for 15minutes at 4 degrees in a table top centrifuge. Clarified lysates werealiquoted to a fresh tube, and protein concentrations for WCL weredetermined by BCA assay (Pierce). Ten micrograms of each lysate wasfractionated on 10-20% Tris-Glycine gel (Biorad), transferred usingiBlot (7 minutes on program 3, using Nitrocellulose transfer stacks),and probed with the following antibodies in Odyssey blocking buffer:SNF5 (CST #8745), EZH2 (CST #5246), and Beta-actin (CST #3700).

In Vitro Cell Assays:

For the adherent cell line proliferation assays (all cell lines exceptKYM-1, which was analyzed as previously described for suspension celllines (Daigle et al., Blood. 2013 Aug. 8; 122(6):1017-25), platingdensities for each cell line were determined based on growth curves(measured by ATP viability) and density over a 7 day timecourse. On theday before compound treatment, cells were plated in either 96-wellplates in triplicate (for the day 0-7 timecourse) or 6-well plates (forreplating on day 7 for the remainder of the timecourse). On Day 0, cellswere either untreated, DMSO-treated, or treated with Compound A startingat 10 uM and decreasing in either 3- or 4-fold dilutions. Plates wereread on Day 0, Day 4, and Day 7 using CellTiter-Glo® (Promega), withcompound/media being replenished on Day 4. On Day 7, the 6-well plateswere trypsinized, centrifuged, and resuspended in fresh media forcounting by Vi-Cell. Cells from each treatment were replated at theoriginal density in 96-well plates in triplicate. Cells were allowed toadhere to the plate overnight, and cells were treated as on Day 0. OnDay 7, 11 and 14, plates were read using CellTiter-Glo®, withcompound/media being replenished on Day 11. Averages of triplicates wereused to plot proliferation over the timecourse, and calculate IC₅₀values. For cell cycle and apoptosis, G401 and RD cells were plated in15 cm dishes in duplicate at a density of 1×10⁶ cells per plate. Cellswere incubated with Compound A at 1 uM, in a total of 25 mL, over acourse of 14 days, with cells being split back to original platingdensity on day 4, 7, and 11. Cell cycle analysis and TUNEL assay wereperformed using a Guava® flow cytometer, following the manufacturer'sprotocol.

Gene Expression Analysis:

G401 and RD cells were plated in T-75 flasks at 175,000 cells/flask and117,000 cells/flask respectively and allowed to adhere overnight. On Day0, cells were treated in duplicates with DMSO or 1 uM Compound A. Cellswere harvested and pelleted on Day 2, 4, and 7 with media and compoundbeing replenished on Day 4. Tumor tissue from the G401 xenograft animalsdosed for 21 days (vehicle, 125 mg/kg, and 250 mg/kg (6 animals each)and 500 mg/kg (4 animals) Compound A dose groups) were used for geneexpression analysis. Total mRNA was extracted from cell pellets andtumor tissue using the RNeasy Mini Kit (Qiagen #74106) and reversetranscribed by the High Capacity cDNA Reverse Transcription Kit (AppliedBiosystems (AB) #4368813). RT-PCR was performed by ViiA™ 7 Real-Time PCRSystems (AB) using TaqMan Fast Advanced Master Mix (AB #4444964) andTaqMan primer/probe sets in table below. Gene expression was normalizedto 18S (AB # Hs99999901_s1) and fold change was calculated using theΔΔCt method. For the in vivo samples, the average Ct value+/−SD wasdetermined for each dose group and fold change compared to vehicle dosegroup was calculated using the AACt method.

Gene AB# MYC Hs00153408_m1 EZH2 Hs00172783_m1 PTCH1 Hs00181117_m1 PROM1(CD133) Hs01009250_m1 GLI1 Hs01110766_m1 DOCK4 Hs00206807_m1 PTPRKHs00267788_m1 BIN1 Hs00184913_m1

ELISA:

Histones were isolated from tumors as previously described (Daigle etal) and were prepared in equivalent concentrations (0.5 ng/ul for H3 and4 ng/ul for H3K27Me3) in coating buffer (PBS with 0.05% BSA). Sample orstandard (100 μL) was added in duplicate to two 96-well ELISA plates(Thermo Labsystems, Immulon 4HBX #3885). Histones isolated from G401cells that were treated with DMSO or 10 μmol/L Compound A for 4 dayswere added to control wells at the same histone concentration as thetumor histone samples. The plates were sealed and incubated overnight at4° C. The following day, plates were washed 3 times with 300 μL/wellPBST (PBS with 0.05% Tween 20; 10×PBST, KPL #51-14-02) on a Bio Tekplate washer. Plates were blocked with 300 μL/well of diluent (PBS+2%BSA+0.05% Tween 20), incubated at room temperature for 2 hours, andwashed 3 times with PBST. All antibodies were diluted in diluent. 100uL/well of anti-H3K27Me3 (CST #9733, 50% glycerol stock 1:1000) oranti-total H3 (Abcam # ab1791, 50% glycerol stock 1:10,000) was added toeach plate. Plates were incubated for 90 minutes at room temperature andwashed 3 times with PBST. 100 μL/well of anti-R_(b)-IgG-HRP (CellSignaling Technology, 7074) was added 1:2000 to the H3K27Me3 plate and1:6000 to the H3 plate and incubated for 90 minutes at room temperature.Plates were washed 4 times with PB ST. For detection, 100 μL/well of TMBsubstrate (BioFx Laboratories, # TMBS) was added and plates incubated inthe dark at room temperature for 5 minutes. Reaction was stopped with100 μL/well 1N H2504. Absorbance at 450 nm was read on SpectraMax M5Microplate reader.

Xenograft Study:

All the procedures related to animal handling, care and the treatment inthis study were performed according to the guidelines approved by theInstitutional Animal Care and Use Committee (IACUC) of ShanghaiChemparner following the guidance of the Association for Assessment andAccreditation of Laboratory Animal Care (AAALAC). For the in vivo study,mice were inoculated subcutaneously at the right flank with G-401 tumorcells (5×10⁶/mouse) in 0.2 ml mixture of base media and Matrigel(McCoy's 5A: Matrige1=1:1) for tumor development. The treatments werestarted when the tumor size reached approximately 157 mm3 for the tumorefficacy study (n=16 mice per group). Compound A or vehicle (0.5%NaCMC+0.1% Tween-80 in water) was administered orally BID at a dosevolume of 10 μL/g for either 21 or 28 days. Animal body weights weremeasured every day during the first week, then twice weekly for theremainder of the study. Tumor size was measured twice weekly in twodimensions using a caliper, and the volume was expressed in mm³. ForPK/PD analysis, 8 mice with the largest tumor burden were euthanized fortumor and blood collection after 21 days of dosing. The remaining micecontinued dosing for one more week, and from day 29, treatment wasstopped and the mice were enrolled in a tumor growth delay study. Micewere observed as individuals until they reached the tumor weightendpoint (2000 mm³) or until day 60 (whichever came first).

Pharmacokinetic Analyses:

Dexamethasone was used as internal standard. An aliquot of 30 μL plasmasample was added with 30 μL IS (Dexamethasone, 1000 ng/mL) and 150 μLACN. The mixture was vortexed for 5 min and centrifuged at 14000 rpm for5 min. An aliquot of 2 μL supernatant was injected for LC-MS/MS analysis(Q-trap 3200). For 10-fold diluted plasma samples an aliquot of 3 μLplasma sample was added with 27 μL blank plasma, the dilution factor was10, then added with 30 μL IS (Dexamethasone, 1000 ng/mL) and 150 μL ACN.The mixture was vortexed for 5 min and centrifuged at 14000 rpm for 5min. An aliquot of 2 μL supernatant was injected for LC-MS/MS analysis.Tumor samples were homogenized on Beadbeater® for 30 seconds with 3×PBS(w/v) to obtain a tumor homogenate. An aliquot of 30 μL tumor homogenatesample was added with 30 μL IS (Dexamethasone, 1000 ng/mL) and 150 μLACN. The mixture was vortexed for 5 min and centrifuged at 14000 rpm for5 min. An aliquot of 2 μL supernatant was injected for LC-MS/MSanalysis.

Example 4: General Experimental Procedures NMR

¹H-NMR spectra were taken using CDCl₃ unless otherwise stated and wererecorded at 400 or 500 MHz using a Varian or Oxford instruments magnet(500 MHz) instruments. Multiplicities indicated are s=singlet,d=doublet, t=triplet, q=quartet, quint=quintet, sxt=sextet, m=multiplet,dd=doublet of doublets, dt=doublet of triplets; br indicates a broadsignal.

LCMS and HPLC

Shimadzu LC-Q, Shimadzu LCMS-2010EV or Waters Acquity Ultra PerformanceLC. HPLC: Products were analyzed by Shimadzu SPD-20A with 150×4.5 mm YMCODS-M80 column or 150×4.6 mm YMC-Pack Pro C18 column at 1.0 ml/min.

Mobile phase was MeCN:H2O=3:2 (containing 0.3% SDS and 0.05% H₃PO₄),

0.05% TFA in water, 0.05% TFA in acetonitrile (gradient Initial 20%,then 0.05% TFA/MeCN to conc. to 95% in 3 min. holds for 0.5 min. at 3.51to 4.50 min then 0.05% TFA/MeCN conc. 20%).

Alternatively the LCMS, 2 different methods were used; the one we usethe most is the high pH (METCR1600) and the other one for more standardcompounds (METCR1416).

0.1% Formic acid in water—Mobile phase “A” 0.1% Formic acid inacetonitrile—Mobile phase “B” utilizing Waters Atlantis dC18, 2.1 mm×100mm, 3 μm column, with a flow rate=0.6 ml/min Column temperature=40° C.;Time (mins) % B 0.00 min 5% B. 5.0 mins 100% B, 5.4 mins 100% B and 0.42mins 5% B

3.5 minute method refers to Atlantis dC18, 2.1 mm×50 mm, 3 μm column,flow rate of 1 ml/min at 40C. Mobile phase A Formic acid (aq.) 0.1%mobile phase B formic acid (MeCN) 0.1%, injection 3 μL, gradient 0 mins(5% organic), 2.5 min (100% organic), 2.7 mins (100% organic), 2.71 min(5% organic), 3.5 min (5% organic)

7.0 minute method refers to Atlantis dC18, 2.1 mm×100 mm, 3 μm column,flow rate of 0.6 ml/min at 40C. Mobile phase A Formic acid (aq.) 0.1%mobile phase B formic acid (MeCN) 0.1%, injection 3 μL, gradient 0 mins(5% organic), 5 min (100% organic), 5.4 mins (100% organic), 5.42 min(5% organic), 7 min (5% organic)

Both the 3. 5 and 7 minute methods were performed on a MS18 ShimadzuLCMS-2010EV or a MS19 Shimadzu LCMS-2010EV system utilizing LC-20ABpumps and SPD-M20A PDA detectors.

Products were purified by HPLC/MS using Waters AutoPurification Systemwith 3100 Mass Detector.

HPLC analyses may also be performed on a Shimdazu LC-2010CHT using anYMC ODS-A, C18, (150×4.6×5 μm) column at ambient temperature with a flowRate of 1.4 ml/min. An injection volume of 10 μl is utilized anddetection occurs via UV/PDA. Mobile Phase A is 0.05 TFA in water andMobile Phase B is 0.05 TFA in acetonitrile with a gradient program ofInitial 5% B to 95% B in 8 min, hold for 1.5 min, at 9.51 to 12 min B.conc. 0.5%. The diluent is the mobile phase

OTHER

Automated flash column chromatography was performed on a Biotage Isoleraversion 4. 10 g SNAP cartridge running at 12 ml/min or a 25 g SNAPcartridge running at 25 ml/min and detecting at 254 nm and 280 nm.

Select Nitrile reductions may be performed on a ThalesNano H-Cube®according to the conditions described in the experimental procedure.

Other related general procedures can also be found in PCT publicationNo. WO12/118812, PCT application No. PCT/US2012/033648 and PCTapplication No. PCT/US2012/033662, each of which is incorporated hereinby reference in its entirety.

Example 5: Synthesis ofN((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(ethyl(tetrahydro-2H-pyran-4-yl)amino)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide

Step 1: Synthesis of 5-bromo-2-methyl-3-nitrobenzoic Acid

To stirred solution of 2-methyl-3-nitrobenzoic acid (100 g, 552 mmol) inconc. H₂SO₄ (400 mL), 1,3-dibromo-5,5-dimethyl-2,4-imidazolidinedione(88 g, 308 mmol) was added in a portion wise manner at room temperatureand the reaction mixture was then stirred at room temperature for 5 h.The reaction mixture was poured onto ice cold water, the precipitatedsolid was filtered off, washed with water and dried under vacuum toafford the desired compound as a solid (140 g, 98%). The isolatedcompound was taken directly into the next step. ¹H NMR (DMSO-d₆, 400MHz) δ 8.31 (s, 1H), 8.17 (s, 1H), 2.43 (s, 3H).

Step 2: Synthesis of methyl 5-bromo-2-methyl-3-nitrobenzoate

To a stirred solution of 5-bromo-2-methyl-3-nitrobenzoic acid (285 g,1105 mmol) in DMF (2.8 L) at room temperature was added sodium carbonate(468 g, 4415 mmol) followed by addition of methyl iodide (626.6 g, 4415mmol). The resulting reaction mixture was heated at 60° C. for 8 h.After completion (monitored by TLC), the reaction mixture was filtered(to remove sodium carbonate) and washed with ethyl acetate (1L×3). Thecombined filtrate was washed with water (3L×5) and the aqueous phase wasback extracted with ethyl acetate (1L×3). The combined organic layerswere dried over anhydrous sodium sulfate, filtered and concentratedunder reduced pressure to afford the title compound as a solid (290 g,97% yield). The isolated compound was taken directly into the next step.¹H NMR (CDCl₃, 400 MHz) δ 8.17 (s, 1H), 7.91 (s, 1H), 3.96 (s, 3H), 2.59(s, 3H).

Step 3: Synthesis of methyl 3-amino-5-bromo-2-methylbenzoate

To a stirred solution of methyl 5-bromo-2-methyl-3-nitrobenzoate (290 g,1058 mmol) in ethanol (1.5 L) was added aqueous ammonium chloride (283g, 5290 mmol dissolved in 1.5 L water). The resulting mixture wasstirred at 80° C. to which iron powder (472 g, 8451 mmol) was added in aportion wise manner. The resulting reaction mixture was heated at 80° C.for 12 h. Upon completion as determined by TLC, the reaction mixture washot filtered over Celite® and the celite bed was washed with methanol (5L) followed by washing with 30% MeOH in DCM (5 L). The combined filtratewas concentrated in-vacuo, the residue obtained was diluted with aqueoussodium bicarbonate solution (2 L) and extracted with ethyl acetate(5L×3). The combined organic layers were dried over anhydrous sodiumsulfate, filtered and concentrated under reduced pressure to afford thetitle compound as a solid (220 g, 85%). The compound was taken directlyinto the next step. ¹H NMR (CDCl₃, 400 MHz) δ 7.37 (s, 1H), 6.92 (s,1H), 3.94 (s, 3H), 3.80 (bs, 2H), 2.31 (s, 3H).

Step 4: Synthesis of methyl5-bromo-2-methyl-3-((tetrahydro-2H-pyran-4-yl) amino) benzoate

To a stirred solution of methyl 3-amino-5-bromo-2-methylbenzoate(15 g,61.5 mmol) and dihydro-2H-pyran-4(3)-one (9.2 g, 92 mmol) indichloroethane (300 mL) was added acetic acid (22 g, 369 mmol) and thereaction mixture stirred at room temperature for 15 minutes, then thereaction mixture was cooled to 0° C. and sodium triacetoxyborohydride(39 g, 184 mmol) was added. The reaction mixture was stirred overnightat room temperature. Upon completion of the reaction as determined byTLC, aqueous sodium bicarbonate solution was added to the reactionmixture until a pH of 7-8 was obtained. The organic phase was separatedand the aqueous phase was extracted with ethyl acetate. The combinedorganic layers were dried over anhydrous sodium sulfate, filtered andconcentrated under reduced pressure. The crude compound was purified bycolumn chromatography (100-200 mesh silica gel) eluting with ethylacetate: hexane to afford the desired compound as a solid (14 g, 69%).¹H NMR (DMSO-d₆, 400 MHz) δ 7.01 (s, 1H), 6.98 (s, 1H), 5.00 (d, 1H,J=7.6 Hz), 3.84-3.87 (m, 2H), 3.79 (s, 3H), 3.54-3.56 (m, 1H), 3.43 (t,2H, J=12 Hz), 2.14 (s, 3H), 1.81-1.84 (m, 2H), 1.47-1.55 (m, 2H).

Step 5: Synthesis of methyl 5-bromo-3-(ethyl (tetrahydro-2H-pyran-4-yl)amino)-2-methylbenzoate

To a stirred solution of methyl5-bromo-2-methyl-3-((tetrahydro-2H-pyran-4-yl) amino) benzoate (14 g,42.7 mmol) in dichloroethane (150 mL) was added acetaldehyde (3.75 g,85.2 mmol) and acetic acid (15.3 g, 256 mmol). The resulting reactionmixture was stirred at room temperature for 15 minutes. The mixture wascooled to 0° C. and sodium triacetoxyborohydride (27 g, 128 mmol) wasadded. The reaction mixture was stirred at room temperature for 3 hours.Upon completion of the reaction as determined by TLC, aqueous sodiumbicarbonate solution was added to the reaction mixture until a pH 7-8was obtained, the organic phase was separated and the aqueous phase wasextracted with ethyl acetate. The combined organic layers were driedover anhydrous sodium sulfate, filtered and concentrated under reducedpressure. The crude compound was purified by column chromatography(100-200 mesh silica gel) eluting with ethyl acetate: hexane to affordthe desired compound as a viscous liquid (14 g, 93%). ¹H NMR (DMSO-d₆,400 MHz) δ 7.62 (s, 1H), 7.52 (s, 1H), 3.80 (bs, 5H), 3.31 (t, 2H),2.97-3.05 (m, 2H), 2.87-2.96 (m, 1H), 2.38 (s, 3H), 1.52-1.61 (m, 2H),1.37-1.50 (m, 2H), 0.87 (t, 3H, J=6.8 Hz).

Step 6: Synthesis of 5-bromo-N-((4, 6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl) methyl)-3-(ethyl (tetrahydro-2H-pyran-4-yl)amino)-2-methylbenzamide

To a stirred solution of 5-bromo-3-(ethyl (tetrahydro-2H-pyran-4-yl)amino)-2-methylbenzoate (14 g, 39.4 mmol) in ethanol (100 mL) was addedaqueous NaOH (2.36 g, 59.2 mmol in 25 mL water) and the resultingmixture was stirred at 60° C. for 1 h. Upon completion of the reactionas determined by TLC, the solvent was removed under reduced pressure andthe residue obtained was acidified with 1N HCl until a pH 7 was obtainedand then aqueous citric acid solution was added until a pH 5-6 wasobtained. The aqueous layer was extracted with 10% MeOH in DCM (200mL×3), the combined organic layers were dried over anhydrous sodiumsulfate, filtered and concentrated under reduced pressure to give therespective acid (14 g, 100%).

The above acid (14 g, 40.9 mmol) was then dissolved in DMSO (70 mL) and3-(amino methyl)-4, 6-dimethylpyridin-2(1H)-one (12.4 g, 81.9 mmol) wasadded to it. The reaction mixture was stirred at room temperature for 15minutes, then PYBOP (31.9 g, 61.4 mmol) was added and stirring wascontinued for overnight at room temperature. Upon completion of thereaction as determined by TLC, the reaction mixture was poured ontoice-cold water (700 mL), stirred for 30 minutes and the precipitatedsolid was collected by filtration, washed with water (500 mL) and airdried. The solid obtained was stirred with acetonitrile (75 mL×2),filtered and air dried. The solid obtained was again stirred with 5%MeOH in DCM (100 mL), filtered and dried completely under vacuum toafford the title compound as a solid (14 g, 74%). ¹H NMR (DMSO-d₆, 400MHz) δ 11.47 (s, 1H), 8.23 (t, 1H), 7.30 (s, 1H), 7.08 (s, 1H), 5.85 (s,1H), 4.23 (d, 2H, J=4.4 Hz), 3.81 (d, 2H, J=10.4 Hz), 3.20-3.26 (m, 2H),3.00-3.07 (m, 1H), 2.91-2.96 (m, 2H), 2.18 (s, 3H), 2.14 (s, 3H), 2.10(s, 3H), 1.58-1.60 (m, 2H), 1.45-1.50 (m, 2H), 0.78 (t, 3H, J=6.8 Hz).

Step 7: Synthesis of N-((4, 6-dimethyl-2-oxo-1, 2-dihydropyridin-3-yl)methyl)-5-(ethyl (tetrahydro-2H-pyran-4-yl)amino)-4-methyl-4′-(morpholinomethyl)[1, 1′-biphenyl]-3-carboxamide

To a stirred solution of 5-bromo-N-((4, 6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl) methyl)-3-(ethyl (tetrahydro-2H-pyran-4-yl)amino)-2-methylbenzamide (14 g, 29.5 mmol) in dioxane/water mixture (70mL/14 mL) was added 4-(4-(4, 4, 5, 5-tetramethyl-1, 3,2-dioxaborolan-2-yl) benzyl) morpholine (13.4 g, 44.2 mmol) followed byaddition of Na₂CO₃ (11.2 g, 106.1 mmol). The solution was purged withargon for 15 minutes and then Pd (PPh₃)₄ (3.40 g, 2.94 mmol) was addedand the solution was again purged with argon for a further 10 min. Thereaction mixture was heated at 100° C. for 4 h. After completion(monitored by TLC), the reaction mixture was diluted with water andextracted with 10% MeOH/DCM. The combined organic layers were dried overanhydrous sodium sulphate, filtered and concentrated under reducedpressure. The crude compound was purified by column chromatography(100-200 mesh silica gel) eluting with methanol: DCM to the titlecompound as a solid (12 g, 71%). Analytical Data: LCMS: 573.35 (M+1)⁺;HPLC: 99.5% (@ 254 nm) (R_(t); 3.999; Method: Column: YMC ODS-A 150mm×4.6 mm×5μ; Mobile Phase: A; 0.05% TFA in water/B; 0.05% TFA inacetonitrile; Inj. Vol: 10 μL, Col. Temp.: 30° C.; Flow rate: 1.4mL/min.; Gradient: 5% B to 95% B in 8 min, Hold for 1.5 min, 9.51-12 min5% B); ¹H NMR (DMSO-d₆, 400 MHz) δ 11.46 (s, 1H), 8.19 (t, 1H), 7.57 (d,2H, J=7.2 Hz), 7.36-7.39 (m, 3H), 7.21 (s, 1H), 5.85 (s, 1H), 4.28 (d,2H, J=2.8 Hz), 3.82 (d, 2H, J=9.6 Hz), 3.57 (bs, 4H), 3.48 (s, 2H), 3.24(t, 2H, J=10.8 Hz), 3.07-3.09 (m, 2H), 3.01 (m, 1H), 2.36 (m, 4H), 2.24(s, 3H), 2.20 (s, 3H), 2.10 (s, 3H), 1.64-1.67 (m, 2H), 1.51-1.53 (m,2H), 0.83 (t, 3H, J=6.4 Hz).

Step 8: Synthesis ofN4(4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(ethyl(tetrahydro-2H-pyran-4-yl)amino)-4-methyl-4′-(morpholinomethyl)[1,1′-biphenyl]-3-carboxamideTrihydrochloride

N-((4, 6-dimethyl-2-oxo-1, 2-dihydropyridin-3-yl) methyl)-5-(ethyl(tetrahydro-2H-pyran-4-yl) amino)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide (12 g, 21.0 mmol) was dissolved in methanolicHCl (200 mL) and stirred at room temperature for 3 h. After three hoursof stirring, the reaction mixture was concentrated under reducedpressure. The solid obtained was stirred with ether (100 mL×2) to affordthe desired salt as a solid (11 g, 77%). Analytical Data of the tri-HClsalt: LCMS: 573.40 (M+1)⁺; HPLC: 99.1% (@ 254 nm) (R_(t); 3.961; Method:Column: YMC ODS-A 150 mm×4.6 mm×5μ; Mobile Phase: A; 0.05% TFA inwater/B; 0.05% TFA in acetonitrile; Inj. Vol: 10 μL, Col. Temp.: 30° C.;Flow rate: 1.4 mL/min.; Gradient: 5% B to 95% B in 8 min, Hold for 1.5min, 9.51-12 min 5% B); ¹H NMR (D₂O 400 MHz) δ 7.92 (bs, 1H,) 7.80 (s,1H), 7.77 (d, 2H, J=8 Hz), 7.63 (s, 1H), 7.61 (s, 1H), 6.30 (s, 1H),4.48 (s, 2H), 4.42 (s, 2H), 4.09-4.11 (m, 4H), 3.95-3.97 (m, 2H), 3.77(t, 3H, J=10.4 Hz), 3.44-3.47 (m, 3H), 3.24-3.32 (m, 3H), 2.42 (s, 3H),2.35 (s, 3H), 2.26 (s, 3H), 2.01 (m, 2H), 1.76 (m, 2H), 1.04 (t, 3H,J=6.8 Hz).

Example 6: N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(((1r,4r)-4-(dimethylamino)cyclohexyl)(ethyl)amino)-4-methyl-4′-(morpholinomethyl)[1,1′-biphenyl]-3-carboxamide

Step 1: 5-bromo-2-methyl-3-nitrobenzoic Acid

To stirred solution of 2-methyl-3-nitrobenzoic acid (100 g, 552.48 mmol)in conc. H₂SO₄ (400 mL), 1,3-dibromo-5,5-dimethyl-2,4-imidazolidinedione(87.98 g, 307.70 mmol) was added in a portion-wise manner at roomtemperature. The reaction mixture was then stirred at room temperaturefor 5 h. The reaction mixture was poured into ice cold water, theprecipitated solid collected by filtration, washed with water and driedunder vacuum to afford desired 5-bromo-2-methyl-3-nitrobenzoic acid asoff-white solid (140 g, 97.90% yield). ¹H NMR (DMSO-d₆, 400 MHz) δ 8.31(s, 1H), 8.17 (s, 1H), 2.43 (s, 3H).

Step 2: methyl 5-bromo-2-methyl-3-nitrobenzoate

To a stirred solution of 5-bromo-2-methyl-3-nitrobenzoic acid (285 g,1104.65 mmol) in DMF (2.8 L) was added sodium carbonate (468 g, 4415.09mmol) followed by addition of methyl iodide (626.63 g, 4415 mmol) atroom temperature. The resulting reaction mixture was stirred at 60° C.for 8 h. The reaction mixture was then filtered to remove suspendedsolids which were washed well with ethyl acetate (3×1 L). The combinedfiltrates were washed well with water (5×3 L) and the aqueous phase backextracted with ethyl acetate (3×1 L). The combined organic extractsdried over anhydrous sodium sulfate, filtered and concentrated underreduced pressure to afford methyl 5-bromo-2-methyl-3-nitrobenzoate as anoff-white solid (290 g, 97% yield). ¹H NMR (CDCl₃, 400 MHz) δ 8.17 (s,1H), 7.91 (s, 1H), 3.96 (s, 3H), 2.59 (s, 3H).

Step 3: methyl 3-amino-5-bromo-2-methylbenzoate

To a stirred solution of methyl 5-bromo-2-methyl-3-nitrobenzoate (290 g,1058.39 mmol) in ethanol (1.5 L) was added aqueous ammonium chloride(283 g, 5290 mmol dissolved in 1.5 L water). The resulting mixture wasstirred and heated at 80° C. followed by addition of iron powder (472 g,8451 mmol) in portions at 80° C. The resulting reaction mixture washeated at 80° C. for 12 h. The reaction mixture was then hot filteredthrough Celite® and the Celite® bed washed well methanol (5 L) and thenwith 30% MeOH in DCM (5 L). The combined filtrates were concentrated invacuo and the residue obtained was diluted with aqueous bicarbonate (2L) and extracted with ethyl acetate (3×5 L). The combined organic layerswere dried over anhydrous sodium sulfate, filtered and concentratedunder reduced pressure to afford methyl 3-amino-5-bromo-2-methylbenzoateas a brown solid (220 g, 89.41% yield).

A portion of the product (5 g) was dissolved in hot ethanol (20 mL),insoluble residue filtered off and mother liquor concentrated to obtainmethyl 3-amino-5-bromo-2-methylbenzoate (3.5 g, 70% yield) with HPLCpurity 93.81% as light brown solid. ¹H NMR (CDCl₃, 400 MHz) δ 7.37 (s,1H), 6.92 (s, 1H), 3.94 (s, 3H), 3.80 (bs, 2H), 2.31 (s, 3H).

Step 4: methyl5-bromo-3-(((1r,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)amino)-2-methylbenzoate

To a stirred solution of methyl 3-amino-5-bromo-2-methylbenzoate(5 g,20.5 mmol) and tert-butyl (4-oxocyclohexyl)carbamate (5.69 g, 26.7 mmol)in dichloroethane (50 mL), acetic acid (7.4 g, 123 mmol) was added andthe reaction was stirred at room temperature for 10 minutes. Sodiumtriacetoxyborohydride (13.1 g, 61.7 mmol) was then added at 0° C. andreaction was stirred at room temperature for 16 hours. The reaction wasquenched with aqueous sodium bicarbonate, the organic phase separatedand the aqueous phase extracted with dichloromethane. The combinedorganic layers were dried over anhydrous sodium sulfate and concentratedin vacuo. The crude product was purified by silica gel columnchromatography (100-200 mesh size) eluting with 10% ethyl acetate inhexane to afford 3.5 g of the more polar (trans) isomer, methyl5-bromo-3-(((1r,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)amino)-2-methylbenzoate,as solid (38.46%). ¹H NMR (CDCl₃, 400 MHz) δ 7.21 (s, 1H), 6.80 (s, 1H),4.41 (bs, 1H), 3.85 (s, 3H), 3.60 (m, 1H), 3.45 (m, 1H), 3.20 (m, 1H),2.22 (s, 3H), 2.15 (bs, 2H), 2.05 (bs, 2H), 1.45 (s, 9H), 1.30 (m, 4H).

Step 5: methyl5-bromo-3-(((1r,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)-(ethyl)amino)-2-methylbenzoate

To a stirred solution of methyl5-bromo-3-(((1r,4r)-4-((tert-butoxycarbonyl)amino)-cyclohexyl)(ethyl)amino)-2-methylbenzoate(55 g, 0.124 mol) and acetaldehyde (11 g, 0.25 mol) in dichloroethane(550 mL), acetic acid (44.64 g, 0.744 mol) was added and the reactionmixture stirred at room temperature for 10 minutes. Sodiumtriacetoxyborohydride (79 g, 0.372 mol) was then added at 0° C. and thereaction mixture was stirred at room temperature for 16 hours. Thereaction was quenched with aqueous sodium bicarbonate, the organic phaseseparated and the aqueous phase extracted with dichloromethane. Thecombined extracts were dried over anhydrous sodium sulfate andconcentrated in-vacuo. The crude compound was purified by silica gelcolumn chromatography (100-200 mesh size) eluting with 10% ethyl acetatein hexane to afford 44 g of methyl5-bromo-3-(((1r,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)-(ethyl)amino)-2-methylbenzoate(75.2%) as solid. ¹H NMR (DMSO-d₆, 400 MHz) δ 7.55 (s, 1H), 7.45 (s,1H), 6.65 (d, 1H), 3.80 (s, 3H), 3.15 (bs, 1H), 3.05 (q, 2H), 2.60 (m,1H), 2.30 (s, 3H), 1.75 (m, 4H), 1.40 (m, 2H), 1.35 (s, 9H), 1.10 (m,2H), 0.80 (t, 3H).

Step 6: tert-butyl((1r,4r)-4-((5-bromo-3-(((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)carbamoyl)-2-methylphenyl)(ethyl)amino)cyclohexyl)carbamate

Aqueous NaOH (3.5 g, 0.08 mol in 10 mL H₂O) was added to a solution ofmethyl5-bromo-3-(((1r,4r)-4-((tert-butoxycarbonyl)amino)cyclohexyl)-(ethyl)amino)-2-methylbenzoate(25 g, 0.053 mol) in EtOH (100 mL) and stirred at 60° C. for 1 h. Theethanol was then removed under reduced pressure and acidified to pH 8with dilute HCl and to pH 6 with citric acid. The mixture was extractedwith 10% methanol in DCM (3×200 mL). The combined organic layers weredried and concentrated giving the respective acid (24.2 g, 99.0%). ¹HNMR (DMSO-d₆, 400 MHz) δ 13.13 (s, 1H), 7.54 (s, 1H), 7.43 (s, 1H), 6.68(d, 1H), 3.14 (bs, 1H), 3.03 (q, 2H), 2.56 (m, 1H), 2.33 (s, 3H),1.80-1.65 (m, 4H), 1.40 (m, 2H), 1.35 (s, 9H), 1.10 (m, 2H), 0.77 (t,3H).

The acid (24 g, 0.053 mol) was dissolved in DMSO (100 mL) and3-(aminomethyl)-4,6-dimethylpyridin-2(1H)-one (16 g, 0.106 mol) andtriethylamine (5.3 g, 0.053 mol) was added. The reaction mixture wasstirred at room temperature for 15 min before PyBop (41 g, 0.079 mmol)was added and stirring was then continued for overnight at roomtemperature. The reaction mixture was poured into ice water (1 L). Theresulting precipitate was collected by filtration, washed well withwater (2×1 L) and dried. The product obtained was further purified bywashings with acetonitrile (3×200 mL) and DCM (100 mL) to affordtert-butyl((1r,4r)-4-((5-bromo-3-(((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)carbamoyl)-2-methylphenyl)(ethyl)amino)cyclohexyl)-carbamate(24 g, 77%). NMR (DMSO-d₆, 400 MHz) δ 11.47 (s, 1H), 8.24 (t, 1H), 7.25(s, 1H), 7.04 (s, 1H), 6.67 (d, 1H), 5.85 (s, 1H), 4.24 (d, 2H), 3.13(bs, 1H), 3.01 (q, 2H), 2.53 (m, 1H), 2.18 (s, 3H), 2.10 (s, 6H),1.80-1.65 (m, 4H), 1.40 (m, 2H), 1.35 (s, 9H), 1.10 (m, 2H), 0.77 (t,3H).

Step 7: tert-butyl((1r,4r)-4-((5-(((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)carbamoyl)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-yl)(ethyl)amino)cyclohexyl)carbamate

To a stirred solution of tert-butyl((1r,4r)-4-((5-bromo-3-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)carbamoyl)-2-methylphenyl)(ethyl)amino)cyclohexyl)-carbamate(24 g, 0.041 mol) and4-(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl)morpholine (18g, 0.061 mol) in dioxane/water mixture (160 mL+40 mL), Na₂CO₃ (15 g,0.15 mol) was added and solution purged with argon for 15 min. Pd(PPh₃)₄(4.7 g, 0.041 mol) was then added and the reaction mixture again purgedwith argon for 10 min. The reaction mixture was heated at 100° C. for 4h. The reaction mixture was then diluted with 10% MeOH/DCM (500 mL) andfiltered. The filtrate was concentrated, diluted with water (500 mL) andextracted with 10% MeOH in DCM (3×500 mL). The combined organic layerswere dried over Na₂SO₄ and solvent removed under reduced pressure. Thecrude product was purified by silica gel column chromatography (100-200mesh) eluting with 7% MeOH in DCM to afford tert-butyl((1r,4r)-4-((5-(((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)carbamoyl)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-yl)(ethyl)amino)cyclohexyl)carbamate(20 g, 71.43%). ¹H NMR (DMSO-d₆, 400 MHz) δ 11.46 (s, 1H), 8.20 (t, 1H),7.56 (d, 2H), 7.36 (m, 3H), 7.17 (s, 1H), 6.66 (d, 1H), 5.85 (s, 1H),4.28 (d, 2H), 3.57 (bs, 4H), 3.48 (s, 2H), 3.20-3.05 (m, 3H), 2.62 (m,1H), 2.36 (bs, 4H), 2.20 (s, 6H), 2.10 (s, 3H), 1.75 (m, 4H), 1.42 (m,2H), 1.35 (s, 9H), 1.10 (m, 2H), 0.82 (t, 3H).

Step 8:5-(((1r,4r)-4-aminocyclohexyl)(ethyl)amino)-N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide

To a stirred solution of tert-butyl((1r,4r)-4-((5-(((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)carbamoyl)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-yl)(ethyl)amino)cyclohexyl)carbamate(20 g, 0.03 mol) in DCM (200 mL) at 0° C., TFA (75 mL) was added andreaction was stirred for 2 h at room temperature. The reaction mixturewas then concentrated to dryness and the residue basified with aqueoussaturated bicarbonate solution (300 mL) to pH 8. The mixture wasextracted with 20% methanol in DCM (4×200 m). The combined extracts weredried over Na₂SO₄ and the solvent removed under reduced pressure toafford5-(((1r,4r)-4-aminocyclohexyl)(ethyl)amino)-N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide(15.5 g, 91%) which was used as is in the next reaction. ¹H NMR(DMSO-d₆, 400 MHz) δ 8.18 (bs, 1H), 7.57 (d, 2H), 7.38 (m, 3H), 7.20 (s,1H), 5.85 (s, 1H), 4.29 (d, 2H), 3.57 (bs, 4H), 3.48 (s, 2H), 3.31 (bs,2H), 3.10 (m, 2H), 2.91 (m, 1H), 2.67 (m, 1H), 2.36 (bs, 4H), 2.21 (s,3H), 2.20 (s, 3H), 2.10 (s, 3H), 1.90 (m, 2H), 1.83 (m, 2H), 1.45 (m,2H), 1.23 (m, 2H), 0.83 (t, 3H).

Step 9:N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-5-(((1r,4r)-4-(dimethylamino)cyclohexyl)(ethyl)amino)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide

To a stirred solution of5-(((1r,4r)-4-aminocyclohexyl)(ethyl)amino)-N-((4,6-dimethyl-2-oxo-1,2-dihydropyridin-3-yl)methyl)-4-methyl-4′-(morpholinomethyl)-[1,1′-biphenyl]-3-carboxamide(14g, 0.023 mol) in dichloromethane (150 mL) was added aqueous 35%formaldehyde solution (2.4 g, 0.080 mol) at 0° C. After stirring for 20min, Na(OAc)₃BH (12.2 g, 0.057 mol) was added and stirring continued for2 h at 0° C. Water (100 mL) was then added to the reaction mixture andthe mixture extracted with 20% methanol in DCM (3×200 mL). The combinedextracts were dried over Na₂SO₄ and the solvent removed under reducedpressure. The crude product was purified by basic alumina columnchromatography eluting with 6-7% MeOH in DCM to afford the titlecompound (10 g, 63.6%). LCMS: 614.65 (M+1)⁺; HPLC: 98.88% (@ 210-370 nm)(R_(t); 3.724; Method: Column: YMC ODS-A 150 mm×4.6 mm×5 μ; MobilePhase: A; 0.05% TFA in water/B; 0.05% TFA in acetonitrile; Inj. Vol: 10μL, Col. Temp.: 30° C.; Flow rate: 1.4 mL/min.; Gradient: 5% B to 95% Bin 8 min, Hold for 1.5 min, 9.51-12 min 5% B); ¹H NMR (DMSO-d₆, 400 MHz)δ 11.45 (s, 1H), 8.17 (t, 1H), 7.56 (d, 2H, J=8 Hz), 7.36 (m, 3H), 7.17(s, 1H), 5.85 (s, 1H), 4.29 (d, 2H, J=4.4 Hz), 3.57 (bs, 4H), 3.48 (s,2H), 3.09 (q, 2H), 2.66 (m, 1H), 2.36 (bs, 4H), 2.21 (s, 3H), 2.20 (s,3H), 2.11 (s, 9H), 1.79 (m, 4H), 1.36 (m, 2H), 1.11 (m, 2H), 0.82 (t,3H, J=6.4&6.8 Hz).

Example 7: Bioassay Protocol and General Methods Protocol for Wild-Typeand Mutant PRC2 Enzyme Assays

General Materials.

S-adenosylmethionine (SAM), S-adenosylhomocyteine (SAH), bicine, KCl,Tween20, dimethylsulfoxide (DMSO) and bovine skin gelatin (BSG) werepurchased from Sigma-Aldrich at the highest level of purity possible.Dithiothreitol (DTT) was purchased from EMD. ³H-SAM was purchased fromAmerican Radiolabeled Chemicals with a specific activity of 80 Ci/mmol.384-well streptavidin Flashplates were purchased from PerkinElmer.

Substrates.

Peptides representative of human histone H₃ residues 21-44 containingeither an unmodified lysine 27 (H₃K27me0) or dimethylated lysine 27(H₃K27me2) were synthesized with a C-terminal G(K-biotin)linker-affinity tag motif and a C-terminal amide cap by 21^(st) CenturyBiochemicals. The peptides were high-performance liquid chromatography(HPLC) purified to greater than 95% purity and confirmed by liquidchromatography mass spectrometry (LC-MS). The sequences are listedbelow.

H3K27me0: (SEQ ID NO: 13) ATKAARKSAPATGGVKKPHRYRPGGK(biotin)-amideH3K27me2: (SEQ ID NO: 14) ATKAARK(me2)SAPATGGVKKPHRYRPGGK(biotin)-amide

Chicken erythrocyte oligonucleosomes were purified from chicken bloodaccording to established procedures.

Recombinant PRC2 Complexes.

Human PRC2 complexes were purified as 4-component enzyme complexesco-expressed in Spodoptera frugiperda (sf9) cells using a baculovirusexpression system. The subunits expressed were wild-type EZH2(NM_004456) or EZH2 Y641F, N, H, S or C mutants generated from thewild-type EZH2 construct, EED (NM_003797), Suz12 (NM_015355) and RbAp48(NM_005610). The EED subunit contained an N-terminal FLAG tag that wasused to purify the entire 4-component complex from sf9 cell lysates. Thepurity of the complexes met or exceeded 95% as determined by SDS-PAGEand Agilent Bioanalyzer analysis. Concentrations of enzyme stockconcentrations (generally 0.3-1.0 mg/mL) was determined using a Bradfordassay against a bovine serum albumin (BSA) standard.

General Procedure for PRC2 Enzyme Assays on Peptide Substrates.

The assays were all performed in a buffer consisting of 20 mM bicine(pH=7.6), 0.5 mM DTT, 0.005% BSG and 0.002% Tween20, prepared on the dayof use. Compounds in 100% DMSO (1 μL) were spotted into polypropylene384-well V-bottom plates (Greiner) using a Platemate 2×3 outfitted witha 384-channel pipet head (Thermo). DMSO (1 μL) was added to columns 11,12, 23, 24, rows A-H for the maximum signal control, and SAH, a knownproduct and inhibitor of PRC2 (1 μL) was added to columns 11, 12, 23,24, rows I-P for the minimum signal control. A cocktail (40 μL)containing the wild-type PRC2 enzyme and H₃K27me0 peptide or any of theY641 mutant enzymes and H₃K27me2 peptide was added by Multidrop Combi(Thermo). The compounds were allowed to incubate with PRC2 for 30 min at25° C., then a cocktail (10 μL) containing a mixture of non-radioactiveand ³H-SAM was added to initiate the reaction (final volume=51 μL). Inall cases, the final concentrations were as follows: wild-type or mutantPRC2 enzyme was 4 nM, SAH in the minimum signal control wells was 1 mMand the DMSO concentration was 1%. The final concentrations of the restof the components are indicated in Table 7, below. The assays werestopped by the addition of non-radioactive SAM (10 μL) to a finalconcentration of 600 μM, which dilutes the ³H-SAM to a level where itsincorporation into the peptide substrate is no longer detectable. 50 μLof the reaction in the 384-well polypropylene plate was then transferredto a 384-well Flashplate and the biotinylated peptides were allowed tobind to the streptavidin surface for at least 1 h before being washedthree times with 0.1% Tween20 in a Biotek ELx405 plate washer. Theplates were then read in a PerkinElmer TopCount platereader to measurethe quantity of ³H-labeled peptide bound to the Flashplate surface,measured as disintegrations per minute (dpm) or alternatively, referredto as counts per minute (cpm).

TABLE 7 Final concentrations of components for each assay variationbased upon EZH2 identity (wild-type or Y641 mutant EZH2) PRC2 Enzyme(denoted by EZH2 Peptide Non-radioactive SAM ³H-SAM identity) (nM) (nM)(nM) Wild-type 185 1800 150 Y641F 200 850 150 Y641N 200 850 150 Y641H200 1750 250 Y641S 200 1300 200 Y641C 200 3750 250

General Procedure for Wild-Type PRC2 Enzyme Assay on OligonucleosomeSubstrate.

The assays was performed in a buffer consisting of 20 mM bicine(pH=7.6), 0.5 mM DTT, 0.005% BSG, 100 mM KCl and 0.002% Tween20,prepared on the day of use. Compounds in 100% DMSO (1 μL) were spottedinto polypropylene 384-well V-bottom plates (Greiner) using a Platemate2×3 outfitted with a 384-channel pipet head (Thermo). DMSO (1 μL) wasadded to columns 11, 12, 23, 24, rows A-H for the maximum signalcontrol, and SAH, a known product and inhibitor of PRC2 (1 μL) was addedto columns 11, 12, 23, 24, rows I-P for the minimum signal control. Acocktail (40 μL) containing the wild-type PRC2 enzyme and chickenerythrocyte oligonucleosome was added by Multidrop Combi (Thermo). Thecompounds were allowed to incubate with PRC2 for 30 min at 25° C., thena cocktail (10 μL) containing a mixture of non-radioactive and ³H-SAMwas added to initiate the reaction (final volume=51 μL). The finalconcentrations were as follows: wild-type PRC2 enzyme was 4 nM,non-radioactive SAM was 430 nM, ³H-SAM was 120 nM, chicken erythrocyteolignonucleosome was 120 nM, SAH in the minimum signal control wells was1 mM and the DMSO concentration was 1%. The assay was stopped by theaddition of non-radioactive SAM (10 μL) to a final concentration of 600μM, which dilutes the ³H-SAM to a level where its incorporation into thechicken erythrocyte olignonucleosome substrate is no longer detectable.50 μL of the reaction in the 384-well polypropylene plate was thentransferred to a 384-well Flashplate and the chicken erythrocytenucleosomes were immobilized to the surface of the plate, which was thenwashed three times with 0.1% Tween20 in a Biotek ELx405 plate washer.The plates were then read in a PerkinElmer TopCount platereader tomeasure the quantity of ³H-labeled chicken erythrocyte oligonucleosomebound to the Flashplate surface, measured as disintegrations per minute(dpm) or alternatively, referred to as counts per minute (cpm).

% Inhibition Calculation

${\% \mspace{14mu} {inh}} = {100 - {( \frac{{dpm}_{cmpd} - {dpm}_{\min}}{{dpm}_{\max} - {dpm}_{\min}} ) \times 100}}$

Where dpm=disintegrations per minute, cmpd=signal in assay well, and minand max are the respective minimum and maximum signal controls.

Four-Parameter IC₅₀ Fit

$Y = {{Bottom} + \frac{( {{Top} - {Bottom}} )}{1 + ( \frac{X}{{IC}_{50}} )^{{Hill}\mspace{14mu} {Coefficient}}}}$

Where top and bottom are the normally allowed to float, but may be fixedat 100 or 0 respectively in a 3-parameter fit. The Hill Coefficientnormally allowed to float but may also be fixed at 1 in a 3-parameterfit. Y is the % inhibition and X is the compound concentration.

IC₅₀ values for the PRC2 enzyme assays on peptide substrates (e.g., EZH2wild type and Y641F) are presented in Table 8 below.

WSU-DLCL2 Methylation Assay

WSU-DLCL2 suspension cells were purchased from DSMZ (German Collectionof Microorganisms and Cell Cultures, Braunschweig, Germany).RPMI/Glutamax Medium, Penicillin-Streptomycin, Heat Inactivated FetalBovine Serum, and D-PBS were purchased from Life Technologies, GrandIsland, N.Y., USA. Extraction Buffer and Neutralization Buffer(5×) werepurchased from Active Motif, Carlsbad, Calif., USA. Rabbit anti-HistoneH₃ antibody was purchased from Abcam, Cambridge, Mass., USA. Rabbitanti-H₃K27me3 and HRP-conjugated anti-rabbit-IgG were purchased fromCell Signaling Technology, Danvers, Mass., USA. TMB “Super Sensitive”substrate was sourced from BioFX Laboratories, Owings Mills, Md., USA.IgG-free Bovine Serum Albumin was purchased from Jackson ImmunoResearch,West Grove, Pa., USA. PBS with Tween (10×PBST) was purchased from KPL,Gaithersburg, Md., USA. Sulfuric Acid was purchased from Ricca Chemical,Arlington, Tex., USA. Immulon ELISA plates were purchased from Thermo,Rochester, N.Y., USA. V-bottom cell culture plates were purchased fromCorning Inc., Corning, N.Y., USA. V-bottom polypropylene plates werepurchased from Greiner Bio-One, Monroe, N.C., USA.

WSU-DLCL2 suspension cells were maintained in growth medium (RPMI 1640supplemented with 10% v/v heat inactivated fetal bovine serum and 100units/mL penicillin-streptomycin) and cultured at 37° C. under 5% CO₂.Under assay conditions, cells were incubated in Assay Medium (RPMI 1640supplemented with 20% v/v heat inactivated fetal bovine serum and 100units/mL penicillin-streptomycin) at 37° C. under 5% CO₂ on a plateshaker.

WSU-DLCL2 cells were seeded in assay medium at a concentration of 50,000cells per mL to a 96-well V-bottom cell culture plate with 200 μL perwell. Compound (1 μL) from 96 well source plates was added directly toV-bottom cell plate. Plates were incubated on a titer-plate shaker at37° C., 5% CO₂ for 96 hours. After four days of incubation, plates werespun at 241×g for five minutes and medium was aspirated gently from eachwell of cell plate without disturbing cell pellet. Pellet wasresuspended in 200 μL DPBS and plates were spun again at 241×g for fiveminutes. The supernatant was aspirated and cold (4° C.) Extractionbuffer (100 μL) was added per well. Plates were incubated at 4° C. onorbital shaker for two hours. Plates were spun at 3427×g×10 minutes.Supernatant (80 μL per well) was transferred to its respective well in96 well V-bottom polypropylene plate. Neutralization Buffer 5× (20 perwell) was added to V-bottom polypropylene plate containing supernatant.V-bottom polypropylene plates containing crude histone preparation (CHP)were incubated on orbital shaker×five minutes. Crude HistonePreparations were added (24, per well) to each respective well intoduplicate 96 well ELISA plates containing 100 μL Coating Buffer(1×PBS+BSA 0.05% w/v). Plates were sealed and incubated overnight at 4°C. The following day, plates were washed three times with 300 μL perwell 1×PBST. Wells were blocked for two hours with 300 μL per well ELISADiluent ((PBS (1×) BSA (2% w/v) and Tween20 (0.05% v/v)). Plates werewashed three times with 1×PBST. For the Histone H₃ detection plate, 100per well were added of anti-Histone-H₃ antibody (Abcam, ab1791) diluted1:10,000 in ELISA Diluent. For H₃K27 trimethylation detection plate, 100μL per well were added of anti-H₃K27me3 diluted 1:2000 in ELISA diluent.Plates were incubated for 90 minutes at room temperature. Plates werewashed three times with 300 μL 1×PBST per well. For Histone H₃detection, 100 μL of HRP-conjugated anti-rabbit IgG antibody diluted to1:6000 in ELISA diluent was added per well. For H₃K27me3 detection, 100μL of HRP conjugated anti-rabbit IgG antibody diluted to 1:4000 in ELISAdiluent was added per well. Plates were incubated at room temperaturefor 90 minutes. Plates were washed four times with 1×PBST 300 μL perwell. TMB substrate 100 μL was added per well. Histone H₃ plates wereincubated for five minutes at room temperature. H₃K27me3 plates wereincubated for 10 minutes at room temperature. The reaction was stoppedwith sulfuric acid 1N (100 μL per well). Absorbance for each plate wasread at 450 nm.

First, the ratio for each well was determined by:

$( \frac{H\; 3K\; 27{me}\; 3\mspace{14mu} {OD}\; 450\mspace{14mu} {value}}{{Histone}\mspace{14mu} H\; 3\mspace{14mu} {OD}\; 450\mspace{14mu} {value}} )$

Each plate included eight control wells of DMSO only treatment (MinimumInhibition) as well as eight control wells for maximum inhibition(Background wells).

The average of the ratio values for each control type was calculated andused to determine the percent inhibition for each test well in theplate. Test compound was serially diluted three-fold in DMSO for a totalof ten test concentrations, beginning at 25 μM. Percent inhibition wasdetermined and IC₅₀ curves were generated using duplicate wells perconcentration of compound. IC₅₀ values for this assay are presented inTable 8 below.

${{Percent}\mspace{14mu} {Inhibition}} = {100 - ( {( \frac{\begin{matrix}{( {{Individual}\mspace{14mu} {Test}\mspace{14mu} {Sample}\mspace{14mu} {Ratio}} ) -} \\( {{Background}\mspace{14mu} {Avg}\mspace{14mu} {Ratio}} )\end{matrix}}{\begin{matrix}{( {{Minimum}\mspace{14mu} {Inhibition}\mspace{14mu} {Ratio}} ) -} \\( {{Background}\mspace{14mu} {Average}\mspace{14mu} {Ratio}} )\end{matrix}} )*100} )}$

Cell Proliferation Analysis

WSU-DLCL2 suspension cells were purchased from DSMZ (German Collectionof Microorganisms and Cell Cultures, Braunschweig, Germany).RPMI/Glutamax Medium, Penicillin-Streptomycin, Heat Inactivated FetalBovine Serum were purchased from Life Technologies, Grand Island, N.Y.,USA. V-bottom polypropylene 384-well plates were purchased from GreinerBio-One, Monroe, N.C., USA. Cell culture 384-well white opaque plateswere purchased from Perkin Elmer, Waltham, Mass., USA. Cell-Titer Glo®was purchased from Promega Corporation, Madison, Wis., USA. SpectraMaxM5 plate reader was purchased from Molecular Devices LLC, Sunnyvale,Calif., USA.

WSU-DLCL2 suspension cells were maintained in growth medium (RPMI 1640supplemented with 10% v/v heat inactivated fetal bovine serum andcultured at 37° C. under 5% CO₂. Under assay conditions, cells wereincubated in Assay Medium (RPMI 1640 supplemented with 20% v/v heatinactivated fetal bovine serum and 100 units/mL penicillin-streptomycin)at 37° C. under 5% CO₂.

For the assessment of the effect of compounds on the proliferation ofthe WSU-DLCL2 cell line, exponentially growing cells were plated in384-well white opaque plates at a density of 1250 cell/ml in a finalvolume of 50 μl of assay medium. A compound source plate was prepared byperforming triplicate nine-point 3-fold serial dilutions in DMSO,beginning at 10 mM (final top concentration of compound in the assay was20 μM and the DMSO was 0.2%). A 100 nL aliquot from the compound stockplate was added to its respective well in the cell plate. The 100%inhibition control consisted of cells treated with 200 nM finalconcentration of staurosporine and the 0% inhibition control consistedof DMSO treated cells. After addition of compounds, assay plates wereincubated for 6 days at 37° C., 5% CO₂, relative humidity>90% for 6days. Cell viability was measured by quantization of ATP present in thecell cultures, adding 35 μl of CellTiter-Glo®® reagent to the cellplates. Luminescence was read in the SpectraMax M5. The concentrationinhibiting cell viability by 50% was determined using a 4-parametric fitof the normalized dose response curves.

INCORPORATION BY REFERENCE

The entire disclosure of each of the patent documents and scientificarticles referred to herein is incorporated by reference for allpurposes.

All publications and patent documents cited herein are incorporatedherein by reference as if each such publication or document wasspecifically and individually indicated to be incorporated herein byreference. Citation of publications and patent documents is not intendedas an admission that any is pertinent prior art, nor does it constituteany admission as to the contents or date of the same. The inventionhaving now been described by way of written description, those of skillin the art will recognize that the invention can be practiced in avariety of embodiments and that the foregoing description and examplesabove are for purposes of illustration and not limitation of the claimsthat follow.

EQUIVALENTS

The invention can be embodied in other specific forms without departingfrom the spirit or essential characteristics thereof. The foregoingembodiments are therefore to be considered in all respects illustrativerather than limiting on the invention described herein. Scope of theinvention is thus indicated by the appended claims rather than by theforegoing description, and all changes that come within the meaning andrange of equivalency of the claims are intended to be embraced therein.

1. A method for treating or alleviating a symptom of aSWI/SNF-associated cancer in a subject comprising administering to asubject in need thereof a therapeutically effective amount of an EZH2inhibitor, wherein the subject has a cancer selected from the groupconsisting of brain and central nervous system cancer, head and neckcancer, kidney cancer, ovarian cancer, pancreatic cancer, leukemia, lungcancer, lymphoma, myeloma, sarcoma, breast cancer, and prostate cancer.2. The method of claim 1, wherein the SWI/SNF-associated cancer ischaracterized by reduced expression or loss of function of the SWI/SNFcomplex or one or more components of the SWI/SNF complex.
 3. The methodof claim 1, wherein the subject has a cancer selected from the groupconsisting of medulloblastoma, malignant rhabdoid tumor and atypicalteratoid/rhabdoid tumor.
 4. The method of claim 2, wherein the one ormore components are selected from the group consisting of SNF5, ATRX andARID1A.
 5. The method of claim 2, wherein the loss of function is causedby a loss of function mutation resulting from a point mutation, adeletion and/or an insertion.
 6. The method of claim 1, wherein thesubject has a deletion of SNF5.
 7. The method of claim 1, wherein thesubject has a mutation of ATRX selected from the group consisting of asubstitution of asparagine (N) for the wild type residue lysine (K) atamino acid position 688 of SEQ ID NO: 5 (K688N), and a substitution ofisoleucine (I) for the wild type residue methionine (M) at amino acidposition 366 of SEQ ID NO: 5 (M366I).
 8. The method of claim 1, whereinsaid subject has a mutation of ARID1A selected from the group consistingof a nonsense mutation for the wild type residue cysteine (C) at aminoacid position 884 of SEQ ID NO: 11 (C884*), a substitution of lysine (K)for the wild type residue glutamic acid (E) at amino acid position 966(E966K), a nonsense mutation for the wild type residue glutamine (Q) atamino acid position 1411 of SEQ ID NO: 11 (Q1411*), a frame shiftmutation at the wild type residue phenylalanine (F) at amino acidposition 1720 of SEQ ID NO: 11 (F1720fs), a frame shift mutation afterthe wild type residue glycine (G) at amino acid position 1847 of SEQ IDNO: 11 (G1847fs), a frame shift mutation at the wild type residuecysteine (C) at amino acid position 1874 of SEQ ID NO: 11 (C1874fs), asubstitution of glutamic acid (E) for the wild type residue asparticacid (D) at amino acid position 1957 (D1957E), a nonsense mutation forthe wild type residue glutamine (Q) at amino acid position 1430 of SEQID NO: 11 (Q1430*), a frame shift mutation at the wild type residuearginine (R) at amino acid position 1721 of SEQ ID NO: 11 (R1721fs), asubstitution of glutamic acid (E) for the wild type residue glycine (G)at amino acid position 1255 (G1255E), a frame shift mutation at the wildtype residue glycine (G) at amino acid position 284 of SEQ ID NO: 11(G284fs), a nonsense mutation for the wild type residue arginine (R) atamino acid position 1722 of SEQ ID NO: 11 (R1722*), a frame shiftmutation at the wild type residue methionine (M) at amino acid position274 of SEQ ID NO: 11 (M274fs), a frame shift mutation at the wild typeresidue glycine (G) at amino acid position 1847 of SEQ ID NO: 11(G1847fs), a frame shift mutation at the wild type residue P at aminoacid position 559 of SEQ ID NO: 11 (P559fs), a nonsense mutation for thewild type residue arginine (R) at amino acid position 1276 of SEQ ID NO:11 (R1276*), a frame shift mutation at the wild type residue glutamine(Q) at amino acid position 2176 of SEQ ID NO: 11 (Q2176fs), a frameshift mutation at the wild type residue histidine (H) at amino acidposition 203 of SEQ ID NO: 11 (H203fs), a frame shift mutation at thewild type residue alanine (A) at amino acid position 591 of SEQ ID NO:11 (A591fs), a nonsense mutation for the wild type residue glutamine (Q)at amino acid position 1322 of SEQ ID NO: 11 (Q1322*), a nonsensemutation for the wild type residue serine (S) at amino acid position2264 of SEQ ID NO: 11 (S2264*), a nonsense mutation for the wild typeresidue glutamine (Q) at amino acid position 586 of SEQ ID NO: 11(Q586*), a frame shift mutation at the wild type residue glutamine (Q)at amino acid position 548 of SEQ ID NO: 11 (Q548fs), and a frame shiftmutation at the wild type residue asparagine (N) at amino acid position756 of SEQ ID NO: 11 (N756fs). 9-18. (canceled)
 19. A method of inducingneuronal differentiation, cell cycle inhibition, gene expression ortumor suppression comprising contacting a cell with an EZH2 inhibitor.20. The method of claim 19, wherein the EZH2 inhibitor is in an amountsufficient to increase expression of at least one gene selected from thegroup consisting of CD133, DOCK4, PTPRK, CKDN1A, CDKN2A, and BIN1.
 21. Amethod of inhibiting hedgehog signaling or gene expression comprisingcontacting a cell with an EZH2 inhibitor.
 22. The method of claim 21,wherein the EZH2 inhibitor is in an amount sufficient to reduceexpression of GLI1 and/or PTCH1.
 23. (canceled)
 24. The method of claim19, wherein the EZH2 inhibitor is in an amount sufficient to induceneuronal differentiation, cell cycle inhibition and/or tumorsuppression. 25-26. (canceled)
 27. The method of claim 21, wherein theEZH2 inhibitor is in an amount sufficient to inhibit hedgehog signaling.28. (canceled)
 29. The method of claim 19, wherein the cell comprisesloss of function of SNF5, ARID1A, ATRX, and/or a component of theSWI/SNF complex.
 30. The method of claim 29, wherein the loss offunction is caused by a deletion of SNF5.
 31. The method of claim 19,wherein the cell is a cancer cell.
 32. The method of claim 31, whereinthe cancer is selected from the group consisting of medulloblastoma,malignant rhabdoid tumor, and atypical teratoid rhabdoid tumor.
 33. Themethod of claim 1, wherein the EZH2 inhibitor is:

or pharmaceutically acceptable salt thereof.
 34. The method of claim 1,wherein the EZH2 inhibitor is:

or pharmaceutically acceptable salt thereof.